Dear all,
Has anyone seen this before? I am using bowtie v0.12.7 to align reads from the short read archive which have IDs as follows:
SRR064286.51418 HWI-EAS418:1:5:1357:1070 length=50
In the resultant SAM file where bowtie finds a match, for some reason the ID is truncated to the first space:
SRR064286.51418
However when no match is found the ID is reported in full.
This seems odd, so I would appreciate someone trying to replicate this for me. Below are a couple of reads and a very short sequence to use as a reference. The first read should match but the other should not. Can someone try and align these using bowtie and let me know what you get.
Many thanks in advance.
Reads: Save as test.fq
@SRR064286.10 HWI-EAS418:1:4:1:147 length=50
TGGCTTCTTCTGTCTTCATAAGTTTTTCCAGGCGGTCTTCCAAGTCCAAA
+SRR064286.10 HWI-EAS418:1:4:1:147 length=50
BCBCCCCCCCCA8::>:?:>8!/@:1&7>6@BCBA@CACCA6>!<BB<BA
@SRR064286.11 HWI-EAS418:1:4:1:119 length=50
GGTTGTAGGACAGCATTTCAAGAACTAAACAGAGATGGTTTCGGAACATA
+SRR064286.11 HWI-EAS418:1:4:1:119 length=50
BBABA@BAABB:3707::9</!.B>:76:8;B9BAAAB>BBC<!<BCBB?
Ref: Save as ref.fa and run "bowtie-build ref.fa ref" to make a reference
>testref
ATTTCGATGCGAGCTTATTCGAGGCGTATCGTAGCGAGTGCTAGGGCTAT
TGGCTTCTTCTGTCTTCATAAGTTTTTCCAGGCGGTCTTCCAAGTCCAAA
GCGGATTGCTGATGCGAGCGTAGTCGTAGTGTGCGTATTGCGATTCGATG
Run bowtie with "bowtie --sam ref test.fq test.sam" and check out the SAM file test.sam.
Thanks for your help
Rich
Has anyone seen this before? I am using bowtie v0.12.7 to align reads from the short read archive which have IDs as follows:
SRR064286.51418 HWI-EAS418:1:5:1357:1070 length=50
In the resultant SAM file where bowtie finds a match, for some reason the ID is truncated to the first space:
SRR064286.51418
However when no match is found the ID is reported in full.
This seems odd, so I would appreciate someone trying to replicate this for me. Below are a couple of reads and a very short sequence to use as a reference. The first read should match but the other should not. Can someone try and align these using bowtie and let me know what you get.
Many thanks in advance.
Reads: Save as test.fq
@SRR064286.10 HWI-EAS418:1:4:1:147 length=50
TGGCTTCTTCTGTCTTCATAAGTTTTTCCAGGCGGTCTTCCAAGTCCAAA
+SRR064286.10 HWI-EAS418:1:4:1:147 length=50
BCBCCCCCCCCA8::>:?:>8!/@:1&7>6@BCBA@CACCA6>!<BB<BA
@SRR064286.11 HWI-EAS418:1:4:1:119 length=50
GGTTGTAGGACAGCATTTCAAGAACTAAACAGAGATGGTTTCGGAACATA
+SRR064286.11 HWI-EAS418:1:4:1:119 length=50
BBABA@BAABB:3707::9</!.B>:76:8;B9BAAAB>BBC<!<BCBB?
Ref: Save as ref.fa and run "bowtie-build ref.fa ref" to make a reference
>testref
ATTTCGATGCGAGCTTATTCGAGGCGTATCGTAGCGAGTGCTAGGGCTAT
TGGCTTCTTCTGTCTTCATAAGTTTTTCCAGGCGGTCTTCCAAGTCCAAA
GCGGATTGCTGATGCGAGCGTAGTCGTAGTGTGCGTATTGCGATTCGATG
Run bowtie with "bowtie --sam ref test.fq test.sam" and check out the SAM file test.sam.
Thanks for your help
Rich
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