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Old 11-16-2012, 10:39 PM   #1
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Post bowtie2 output, sam to bam conversion error.

Hi all,

I am trying convert a sam file (PE bowtie2 default fr output) to bam file using samtools view command. But it's throwing the following error.

$ samtools view -bS -o aln3.bam aln3.sam
[samopen] SAM header is present: 17 sequences
[sam_read1] reference '451450' is recognized as '*'
Parse error at line 2026299: sequence and quality are inconsistent
When I looked at the partcular line,
sed -n 2026299p aln3.sam
        133     chr12   451450  0       *       =       451450  0       *       *       YT:Z:UP YF:Z:LN
Its missing col1 (Qname) also CIGAR string, segment sequence and Quality scores are unavailable.

When I checked for such lines
$ sed -n '/^[^H]/=' aln3.sam | wc -l
There were 5422 lines.

How do I proceed now?? Do I delete these 5422 lines from sam file?? This thread here had the same problem but it was with bwa aligner.

Also my bowtie output after aligning says (many such lines are produced before showing final alignment stats):

Warning: skipping mate #2 of read '' because length (0) <= # seed mismatches (0)
Warning: skipping mate #2 of read '' because it was < 2 characters long
I am not able interprte this. Also my alignement stats says 99.97% pairs were aligned concordantly 0 times. I am bit amused.
1018542 reads; of these:
  1018542 (100.00%) were paired; of these:
    1018249 (99.97%) aligned concordantly 0 times
    188 (0.02%) aligned concordantly exactly 1 time
    105 (0.01%) aligned concordantly >1 times
How do I proceed now??

Thank you.

Between I am new to analysis and I hope you people dont mind if my questions are too simple.

Last edited by a_mt; 11-16-2012 at 10:41 PM.
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Old 03-21-2014, 01:27 PM   #2
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Posts: 142
Default Skipping Mate errors

Hello. I have the same issue

Warning: skipping mate #1 of read 'SN860:381:H80WNADXX:1:1101:18171:2118 1:N:0:1' because length (0) <= # seed mismatches (0)
Warning: skipping mate #1 of read 'SN860:381:H80WNADXX:1:1101:18171:2118 1:N:0:1' because it was < 2 characters long
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Old 03-21-2014, 02:59 PM   #3
Brian Bushnell
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Posts: 2,707

It sounds like you have a 0bp read, possibly due to quality trimming. You can try removing such reads (and their mates) with a tool that allows you to specify a minimum read length.
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Old 03-29-2015, 01:23 AM   #4
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I solved this problem after trimming fastaq files with fastx_trimmer -f and fastx_trimmer -t operations with no 0bp read in output files. So the solution for me was to remove artifacts with fastx_artifacts_filter and then synchronize pairs with
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