Multiple index files in Bowtie?

spb2003 · 10-13-2009, 09:52 AM

Hello Everyone,

I am working on a 32 bit RH Linux machine and setting up a RNASeq analysis pipeline. As part of ERANGE, I am building an index of the expanded genome but on including .fa.masked files the total number of characters balloons to more than 2^32. I went ahead and built two index files by splitting all the files into two sets.
I tried an small example of aligning a 36bp read against both the refseq and ensembl index. No alignments are found if I use two index together in the command line but they are found when searched against one index at a time. Is this the only option when there are multiple index files or am I missing something more obvious?

Thanks for your help.

GeeSharpMinor · 10-13-2009, 10:53 AM

I run an RNAseq pipeline where we sequentially align against two different indexes, maybe I can help. can you copy/paste the commands you use, also listing any options?

spb2003 · 10-13-2009, 02:19 PM

for eg. I want to align CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA against two index files hg18_block1 and hg18_block2. Since I am still building the index, I will give an example using different index

$bowtie -t human_ensembl_cdna -c CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:02
Seeded quality full-index search: 00:00:00
0 + ENST00000322310 755 CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 7:T>C,18:C>N
Reported 1 alignments to 1 output stream(s)
Time searching: 00:00:03
Overall time: 00:00:03

$bowtie -t refseq_human -c CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA
Time loading forward index: 00:00:02
Time loading mirror index: 00:00:01
Seeded quality full-index search: 00:00:00
0 + REFSEQ:NM_003731 800 CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 7:T>C,18:C>N
Reported 1 alignments to 1 output stream(s)
Time searching: 00:00:03
Overall time: 00:00:03

The following does not work:
$bowtie -t human_ensembl_cdna -t refseq_human -c CCCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA
Time loading forward index: 00:00:02
Time loading mirror index: 00:00:01
Seeded quality full-index search: 00:00:00
No results
Time searching: 00:00:03
Overall time: 00:00:03

Is a sequential search the only option or is there a way to do alignment against multiple index files simultaneously.

Thanks.

GeeSharpMinor · 10-13-2009, 05:22 PM

unfortunately, sequential is the only way to do it as far as I know.

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10-13-2009, 09:52 AM	#1
spb2003 Junior Member Location: seattle Join Date: Feb 2009 Posts: 4	Multiple index files in Bowtie? Hello Everyone, I am working on a 32 bit RH Linux machine and setting up a RNASeq analysis pipeline. As part of ERANGE, I am building an index of the expanded genome but on including .fa.masked files the total number of characters balloons to more than 2^32. I went ahead and built two index files by splitting all the files into two sets. I tried an small example of aligning a 36bp read against both the refseq and ensembl index. No alignments are found if I use two index together in the command line but they are found when searched against one index at a time. Is this the only option when there are multiple index files or am I missing something more obvious? Thanks for your help.

10-13-2009, 10:53 AM	#2
GeeSharpMinor Junior Member Location: washington Join Date: Mar 2009 Posts: 4	I run an RNAseq pipeline where we sequentially align against two different indexes, maybe I can help. can you copy/paste the commands you use, also listing any options?

10-13-2009, 02:19 PM	#3
spb2003 Junior Member Location: seattle Join Date: Feb 2009 Posts: 4	for eg. I want to align CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA against two index files hg18_block1 and hg18_block2. Since I am still building the index, I will give an example using different index $bowtie -t human_ensembl_cdna -c CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA Time loading forward index: 00:00:01 Time loading mirror index: 00:00:02 Seeded quality full-index search: 00:00:00 0 + ENST00000322310 755 CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 7:T>C,18:C>N Reported 1 alignments to 1 output stream(s) Time searching: 00:00:03 Overall time: 00:00:03 $bowtie -t refseq_human -c CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Seeded quality full-index search: 00:00:00 0 + REFSEQ:NM_003731 800 CCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII 0 7:T>C,18:C>N Reported 1 alignments to 1 output stream(s) Time searching: 00:00:03 Overall time: 00:00:03 The following does not work: $bowtie -t human_ensembl_cdna -t refseq_human -c CCCTCACCCTGTCCCTCCTNAGCCAGCAGAGGCCCA Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Seeded quality full-index search: 00:00:00 No results Time searching: 00:00:03 Overall time: 00:00:03 Is a sequential search the only option or is there a way to do alignment against multiple index files simultaneously. Thanks.

10-13-2009, 05:22 PM	#4
GeeSharpMinor Junior Member Location: washington Join Date: Mar 2009 Posts: 4	unfortunately, sequential is the only way to do it as far as I know.