FusionSeq FAQ - Revision history

Asboner: /* gfrConfidenceValues: Cannot find the .meta file */

2011-07-14T19:22:42Z

gfrConfidenceValues: Cannot find the .meta file

← Older revision		Revision as of 19:22, 14 July 2011
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	==gfrConfidenceValues: Cannot find the .meta file==		==gfrConfidenceValues: Cannot find the .meta file==
	The .meta file is required to run gfrConfidenceValues. This is a tab-delimited file including the number of mapped reads. A simple way to generate this file is to run:		The .meta file is required to run [[FusionSeq_List_of_programs#gfrConfidenceValues\|gfrConfidenceValues]]. This is a tab-delimited file including the number of mapped reads. A simple way to generate this file is to run:
	$ MAPPED=$(grep -v "AlignmentBlock" file.mrf \| grep -v "#" \| wc -l); printf "Mapped_reads\t%d\n" $MAPPED > file.meta		$ MAPPED=$(grep -v "AlignmentBlock" file.mrf \| grep -v "#" \| wc -l); printf "Mapped_reads\t%d\n" $MAPPED > file.meta

Asboner: /* geneFusions: Segmentation Fault */

2011-07-14T19:19:03Z

geneFusions: Segmentation Fault

← Older revision		Revision as of 19:19, 14 July 2011
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	==geneFusions: Segmentation Fault==		==geneFusions: Segmentation Fault==
	There a number of reasons why one gets this error. One possibility is the lack of the sequences in the MRF file. Although MRF does not require the inclusion of sequences to be valid, sequences are indeed required by geneFusions. Please ensure that sequences are present in the MRF file.		There a number of reasons why one gets this error. One possibility is the lack of the sequences in the MRF file. Although MRF does not require the inclusion of sequences to be valid, sequences are indeed required by geneFusions. Please ensure that sequences are present in the MRF file.

			==gfrConfidenceValues: Cannot find the .meta file==
			The .meta file is required to run gfrConfidenceValues. This is a tab-delimited file including the number of mapped reads. A simple way to generate this file is to run:
			$ MAPPED=$(grep -v "AlignmentBlock" file.mrf \| grep -v "#" \| wc -l); printf "Mapped_reads\t%d\n" $MAPPED > file.meta

			The final files should look like:
			Mapped_reads 123456789

	==Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF?==		==Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF?==

Asboner: /* Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF? */

2011-05-19T18:08:59Z

Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF?

← Older revision		Revision as of 18:08, 19 May 2011
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	==Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF?==		==Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF?==
	To convert bowtie alignment into MRF when ends are aligned separately, we require the two ends to be on subsequent lines. This could be partially achieved by concatenating and sorting the two alignment files, e.g. cat end_1.bowtie end_2.bowtie \| sort > alignment.bowtie. However, in some cases, only one end is mapped, thus creating "~~singleton~~" in the alignment file, where only one end is reported. Since there have been many requests regarding this issue, we decided to share an "internal" utility: bowtiePairedFix. Here you can download the binary file:		To convert bowtie alignment into MRF when ends are aligned separately, we require the two ends to be on subsequent lines. This could be partially achieved by concatenating and sorting the two alignment files, e.g. cat end_1.bowtie end_2.bowtie \| sort > alignment.bowtie. However, in some cases, only one end is mapped, thus creating "singletons" in the alignment file, where only one end is reported. Since there have been many requests regarding this issue, we decided to share an "internal" utility: bowtiePairedFix. Here you can download the binary file:

	* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.linux64 bowtiePairedFix (GNU/Linux x86_64)]		* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.linux64 bowtiePairedFix (GNU/Linux x86_64)]

Asboner: /* How can I cite FusionSeq? */

2011-04-25T17:13:41Z

How can I cite FusionSeq?

← Older revision		Revision as of 17:13, 25 April 2011
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	==Where can I find more information?==		==Where can I find more information?==
	The most up-to-date user documentation for FusionSeq is available [[FusionSeq\|here]]. If you look for the developer's documentation, you can find it [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/documentation/index.html here].		The most up-to-date user documentation for FusionSeq is available [[FusionSeq\|here]]. If you look for the developer's documentation, you can find it [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/documentation/index.html here].

			==The BOWTIE_INDEXES directory is used for reference indexes as well as for temporary index files. However, I have a centralized repository of indexed genomes and cannot create the temporary files in that directory==
			A workaround of this issue would be to create a local directory where one has write permission. This would solve the problem of generating temporary index files when running the junction-sequence identifier module. To also have the indexed genome and transcriptome in the same folder, one could link them symbolically, for example:
			$ cd /path/to/local/folder/
			$ ln -s /path/to/centralized/repository/hg18_nh/ .
			$ ln -s /path/to/centralized/repository/hg18_knownGeneAnnotationTranscriptCompositeModel/ .

			Now, BOWTIE_INDEXES in geneFusionConfig.h should point to /path/to/local/folder/ where the user can generate temporary files:
			#define BOWTIE_INDEXES /path/to/local/folder

	==How can I cite FusionSeq?==		==How can I cite FusionSeq?==
	Please cite this publication:		Please cite this publication:
	* Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB. '''FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data'''. ''Genome Biol'' 21 Oct. 2010; '''11''':R104 [http://dx.doi.org/10.1186/gb-2010-11-10-r104\|doi:10.1186/gb-2010-11-10-r104]		* Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB. '''FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data'''. ''Genome Biol'' 21 Oct. 2010; '''11''':R104 [http://dx.doi.org/10.1186/gb-2010-11-10-r104\|doi:10.1186/gb-2010-11-10-r104]


	=Compilation troubleshooting=		=Compilation troubleshooting=

Asboner: /* Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF? */

2011-04-18T14:32:15Z

Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF?

← Older revision		Revision as of 14:32, 18 April 2011
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	* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.MacOs.10.6.7 bowtiePairedFix (MacOs 10.6.7)]		* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.MacOs.10.6.7 bowtiePairedFix (MacOs 10.6.7)]
	The conversion command is:		The conversion command is:
	cat end_1.bowtie end_2.bowtie \| sort \| bowtiePairedFix \| bowtie2mrf paired > data.mrf 2> data.mrf.log		cat end_1.bowtie end_2.bowtie \| sort \| bowtiePairedFix \| bowtie2mrf paired -sequence > data.mrf 2> data.mrf.log

	Please note that this program is also provided "as is".		Please note that this program is also provided "as is".

Asboner: /* Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF? */

2011-04-18T13:26:48Z

Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF?

← Older revision		Revision as of 13:26, 18 April 2011
Line 60:		Line 60:
	To convert bowtie alignment into MRF when ends are aligned separately, we require the two ends to be on subsequent lines. This could be partially achieved by concatenating and sorting the two alignment files, e.g. cat end_1.bowtie end_2.bowtie \| sort > alignment.bowtie. However, in some cases, only one end is mapped, thus creating "singleton" in the alignment file, where only one end is reported. Since there have been many requests regarding this issue, we decided to share an "internal" utility: bowtiePairedFix. Here you can download the binary file:		To convert bowtie alignment into MRF when ends are aligned separately, we require the two ends to be on subsequent lines. This could be partially achieved by concatenating and sorting the two alignment files, e.g. cat end_1.bowtie end_2.bowtie \| sort > alignment.bowtie. However, in some cases, only one end is mapped, thus creating "singleton" in the alignment file, where only one end is reported. Since there have been many requests regarding this issue, we decided to share an "internal" utility: bowtiePairedFix. Here you can download the binary file:

	* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/~~bowtiePairedFix_linux64~~ bowtiePairedFix (GNU/Linux x86_64)]		* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.linux64 bowtiePairedFix (GNU/Linux x86_64)]
	* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.MacOs.10.6.7 bowtiePairedFix (MacOs 10.6.7)]		* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.MacOs.10.6.7 bowtiePairedFix (MacOs 10.6.7)]
	The conversion command is:		The conversion command is:

Asboner: /* Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF? */

2011-04-18T13:26:15Z

Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF?

← Older revision		Revision as of 13:26, 18 April 2011
Line 60:		Line 60:
	To convert bowtie alignment into MRF when ends are aligned separately, we require the two ends to be on subsequent lines. This could be partially achieved by concatenating and sorting the two alignment files, e.g. cat end_1.bowtie end_2.bowtie \| sort > alignment.bowtie. However, in some cases, only one end is mapped, thus creating "singleton" in the alignment file, where only one end is reported. Since there have been many requests regarding this issue, we decided to share an "internal" utility: bowtiePairedFix. Here you can download the binary file:		To convert bowtie alignment into MRF when ends are aligned separately, we require the two ends to be on subsequent lines. This could be partially achieved by concatenating and sorting the two alignment files, e.g. cat end_1.bowtie end_2.bowtie \| sort > alignment.bowtie. However, in some cases, only one end is mapped, thus creating "singleton" in the alignment file, where only one end is reported. Since there have been many requests regarding this issue, we decided to share an "internal" utility: bowtiePairedFix. Here you can download the binary file:

	* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/~~bowtiePairedFix~~ bowtiePairedFix (GNU/Linux x86_64)]		* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix_linux64 bowtiePairedFix (GNU/Linux x86_64)]
	* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.MacOs.10.6.7 bowtiePairedFix (MacOs 10.6.7)]		* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.MacOs.10.6.7 bowtiePairedFix (MacOs 10.6.7)]
	The conversion command is:		The conversion command is:

Asboner: /* Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF? */

2011-04-18T13:25:40Z

Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF?

← Older revision		Revision as of 13:25, 18 April 2011
Line 60:		Line 60:
	To convert bowtie alignment into MRF when ends are aligned separately, we require the two ends to be on subsequent lines. This could be partially achieved by concatenating and sorting the two alignment files, e.g. cat end_1.bowtie end_2.bowtie \| sort > alignment.bowtie. However, in some cases, only one end is mapped, thus creating "singleton" in the alignment file, where only one end is reported. Since there have been many requests regarding this issue, we decided to share an "internal" utility: bowtiePairedFix. Here you can download the binary file:		To convert bowtie alignment into MRF when ends are aligned separately, we require the two ends to be on subsequent lines. This could be partially achieved by concatenating and sorting the two alignment files, e.g. cat end_1.bowtie end_2.bowtie \| sort > alignment.bowtie. However, in some cases, only one end is mapped, thus creating "singleton" in the alignment file, where only one end is reported. Since there have been many requests regarding this issue, we decided to share an "internal" utility: bowtiePairedFix. Here you can download the binary file:

	* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix bowtiePairedFix (~~linux 64bit~~)]		* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix bowtiePairedFix (GNU/Linux x86_64)]
	* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.MacOs.10.6.7 bowtiePairedFix (MacOs 10.6.7)]		* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.MacOs.10.6.7 bowtiePairedFix (MacOs 10.6.7)]
	The conversion command is:		The conversion command is:

Asboner: /* geneFusions: Segmentation Fault */

2011-04-18T13:23:07Z

geneFusions: Segmentation Fault

← Older revision		Revision as of 13:23, 18 April 2011
Line 56:		Line 56:
	==geneFusions: Segmentation Fault==		==geneFusions: Segmentation Fault==
	There a number of reasons why one gets this error. One possibility is the lack of the sequences in the MRF file. Although MRF does not require the inclusion of sequences to be valid, sequences are indeed required by geneFusions. Please ensure that sequences are present in the MRF file.		There a number of reasons why one gets this error. One possibility is the lack of the sequences in the MRF file. Although MRF does not require the inclusion of sequences to be valid, sequences are indeed required by geneFusions. Please ensure that sequences are present in the MRF file.

			==Paired-end reads and bowtie: I aligned each end separately. How do I convert the alignment file to MRF?==
			To convert bowtie alignment into MRF when ends are aligned separately, we require the two ends to be on subsequent lines. This could be partially achieved by concatenating and sorting the two alignment files, e.g. cat end_1.bowtie end_2.bowtie \| sort > alignment.bowtie. However, in some cases, only one end is mapped, thus creating "singleton" in the alignment file, where only one end is reported. Since there have been many requests regarding this issue, we decided to share an "internal" utility: bowtiePairedFix. Here you can download the binary file:

			* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix bowtiePairedFix (linux 64bit)]
			* [http://archive.gersteinlab.org/proj/rnaseq/fusionseq/tarballs/bowtiePairedFix.MacOs.10.6.7 bowtiePairedFix (MacOs 10.6.7)]
			The conversion command is:
			cat end_1.bowtie end_2.bowtie \| sort \| bowtiePairedFix \| bowtie2mrf paired > data.mrf 2> data.mrf.log

			Please note that this program is also provided "as is".

Asboner: /* Compilation troubleshooting */

2011-01-27T21:10:02Z

Compilation troubleshooting

← Older revision		Revision as of 21:10, 27 January 2011
Line 35:		Line 35:

	=Compilation troubleshooting=		=Compilation troubleshooting=

			==Where can I find the BIOS library, required for FusionSeq?==
			As described in [[Requirements]], the [http://rnaseq.gersteinlab.org/doc/bios/ BIOS] library can be downloaded as part of [http://rseqtools.gersteinlab.org RSEQtools], a computational framework to analyze RNA-Seq data, or it can be downloaded as a separate component from [http://rnaseq.gersteinlab.org/fusionseq/tarballs/bios_0.9.0.tar.gz here].

	==TROOT.h: No such file or directory==		==TROOT.h: No such file or directory==
	This error occurs because the compiler does not find TROOT.h file. This file is part of [http://root.cern.ch/drupal/ ROOT], a framework for mathematical and statistical analysis. If you have installed [http://root.cern.ch/drupal/ ROOT], please make sure that you have defined ROOTSYS as the path to the ROOT folder and added it to your PATH:		This error occurs because the compiler does not find TROOT.h file. This file is part of [http://root.cern.ch/drupal/ ROOT], a framework for mathematical and statistical analysis. If you have installed [http://root.cern.ch/drupal/ ROOT], please make sure that you have defined ROOTSYS as the path to the ROOT folder and added it to your PATH:
Line 40:		Line 44:
	$ export PATH=$ROOTSYS/bin:$PATH		$ export PATH=$ROOTSYS/bin:$PATH
	Please also see [[Installation_and_Configuration_of_FusionSeq#Installing_and_configuring_ROOT\|Installing and configuring ROOT]] for more details.		Please also see [[Installation_and_Configuration_of_FusionSeq#Installing_and_configuring_ROOT\|Installing and configuring ROOT]] for more details.


	=Running issues=		=Running issues=