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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.
When I looked at the partcular line,
Its missing col1 (Qname) also CIGAR string, segment sequence and Quality scores are unavailable.
When I checked for such lines
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):
I am not able interprte this. Also my alignement stats says 99.97% pairs were aligned concordantly 0 times. I am bit amused.
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.
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.
Code:
$ 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
Code:
sed -n 2026299p aln3.sam
133 chr12 451450 0 * = 451450 0 * * YT:Z:UP YF:Z:LN
When I checked for such lines
Code:
$ sed -n '/^[^H]/=' aln3.sam | wc -l 5422
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):
Code:
Warning: skipping mate #2 of read '' because length (0) <= # seed mismatches (0) Warning: skipping mate #2 of read '' because it was < 2 characters long
Code:
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
Thank you.
Between I am new to analysis and I hope you people dont mind if my questions are too simple.
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