tophat on paired files

jyli · 10-13-2009, 01:35 PM

Dear all,

I am using tophat and ran into a simple error. When I put in more pairs in the command, it failed complaining not being able to open the files.

Any comment is appreciated...

What was said in the documentation:
******************
<reads1_1[,...,readsN_1]> A comma-separated list of files containing reads in FASTQ or FASTA format. When running TopHat with paired-end reads, this should be the *_1 ("left") set of files.
<[reads1_2,...readsN_2]> A comma-separated list of files containing reads in FASTA or FASTA format. Only used when running TopHat with paired end reads, and contains the *_2 ("right") set of files. The *_2 files *MUST* appear in the same order as the *_1 files.
******************

My command:

********************************************
tophat --solexa1.3-quals -m 1 -r 130 -G /datastore/nextgenproc/projects/exonDB/custom_exonDB.04152009.hg18.exon.gff /home/jyli/Bowtie/indexes/hg18_genome
../raw_data/MCF7_CP7_00300_003_s_4_1.txt, ../raw_data/MCF7_CP7_00300_008_s_7_1.txt ../raw_data/MCF7_CP7_00300_003_s_4_2.txt, ../raw_data/MCF7_CP7_00300_008_s_7_2.txt
****************************************

Error here...
#########################################
[Tue Oct 13 16:10:37 2009] Beginning TopHat run (v1.0.10)
-----------------------------------------------
[Tue Oct 13 16:10:37 2009] Preparing output location ./tophat_out/
[Tue Oct 13 16:10:37 2009] Checking for Bowtie index files
[Tue Oct 13 16:10:37 2009] Checking for reference FASTA file
[Tue Oct 13 16:10:37 2009] Checking for Bowtie
Bowtie version: 0.10.0.2
[Tue Oct 13 16:10:37 2009] Checking reads
Error: could not open file
#############################################

Cole Trapnell · 10-13-2009, 01:59 PM

You appear to have the reads separated by spaces and commas. The left reads should be a single comma separated list, and same for the right. Like this:

tophat --solexa1.3-quals -m 1 -r 130 -G /datastore/nextgenproc/projects/exonDB/custom_exonDB.04152009.hg18.exon.gff /home/jyli/Bowtie/indexes/hg18_genome
../raw_data/MCF7_CP7_00300_003_s_4_1.txt,../raw_data/MCF7_CP7_00300_008_s_7_1.txt ../raw_data/MCF7_CP7_00300_003_s_4_2.txt,../raw_data/MCF7_CP7_00300_008_s_7_2.txt

jyli · 10-14-2009, 07:01 AM

Thank you so much, it worked out properly!

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10-13-2009, 01:35 PM	#1
jyli Member Location: North Carolina Join Date: Nov 2008 Posts: 21	tophat on paired files Dear all, I am using tophat and ran into a simple error. When I put in more pairs in the command, it failed complaining not being able to open the files. Any comment is appreciated... What was said in the documentation: ****************** <reads1_1[,...,readsN_1]> A comma-separated list of files containing reads in FASTQ or FASTA format. When running TopHat with paired-end reads, this should be the _1 ("left") set of files. <[reads1_2,...readsN_2]> A comma-separated list of files containing reads in FASTA or FASTA format. Only used when running TopHat with paired end reads, and contains the _2 ("right") set of files. The _2 files MUST* appear in the same order as the _1 files. *************** My command: **************************************** tophat --solexa1.3-quals -m 1 -r 130 -G /datastore/nextgenproc/projects/exonDB/custom_exonDB.04152009.hg18.exon.gff /home/jyli/Bowtie/indexes/hg18_genome ../raw_data/MCF7_CP7_00300_003_s_4_1.txt, ../raw_data/MCF7_CP7_00300_008_s_7_1.txt ../raw_data/MCF7_CP7_00300_003_s_4_2.txt, ../raw_data/MCF7_CP7_00300_008_s_7_2.txt ************************************** Error here... ######################################### [Tue Oct 13 16:10:37 2009] Beginning TopHat run (v1.0.10) ----------------------------------------------- [Tue Oct 13 16:10:37 2009] Preparing output location ./tophat_out/ [Tue Oct 13 16:10:37 2009] Checking for Bowtie index files [Tue Oct 13 16:10:37 2009] Checking for reference FASTA file [Tue Oct 13 16:10:37 2009] Checking for Bowtie Bowtie version: 0.10.0.2 [Tue Oct 13 16:10:37 2009] Checking reads Error: could not open file #############################################

10-13-2009, 01:59 PM	#2
Cole Trapnell Senior Member Location: Boston, MA Join Date: Nov 2008 Posts: 212	You appear to have the reads separated by spaces and commas. The left reads should be a single comma separated list, and same for the right. Like this: tophat --solexa1.3-quals -m 1 -r 130 -G /datastore/nextgenproc/projects/exonDB/custom_exonDB.04152009.hg18.exon.gff /home/jyli/Bowtie/indexes/hg18_genome ../raw_data/MCF7_CP7_00300_003_s_4_1.txt,../raw_data/MCF7_CP7_00300_008_s_7_1.txt ../raw_data/MCF7_CP7_00300_003_s_4_2.txt,../raw_data/MCF7_CP7_00300_008_s_7_2.txt

10-14-2009, 07:01 AM	#3
jyli Member Location: North Carolina Join Date: Nov 2008 Posts: 21	Thank you so much, it worked out properly!