Blast to SAM

[fznajar]

I converted my BlasyN to SAM using:

blast2sam.pl <blastN file> > <output file>

I then tried to generate a "bam" file using:

samtools view -bT <reference.fasta> <sam file> -o <bam output>


I got the following output:
[sam_header_read2] 0 sequences loaded.
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

Any help?

Thanks in advance

[seqeve]

If the header is absent from the SAM file use the command below, where reference.fa is the reference fasta file used to map the reads:
samtools view -bT reference.fa test.sam > test.bam

If the header information is available:
samtools view -bS test.sam > test.bam

http://davetang.org/wiki/tiki-index.php?page=SAMTools

I would suggest trying -bS, even though this is opposite to what this wiki says?

[fznajar]

Thank you seqeve.
I am still getting the same error above.
Best

[kmcarr]

I converted my BlasyN to SAM using:

blast2sam.pl <blastN file> > <output file>

I then tried to generate a "bam" file using:

samtools view -bT <reference.fasta> <sam file> -o <bam output>


I got the following output:
[sam_header_read2] 0 sequences loaded.
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

Any help?

Thanks in advance

Try providing a reference index file instead of the reference fasta itself.

samtools faidx <reference.fasta> [Creates reference.fasta.fai]

samtools view -bt <reference.fasta.fai> -o <bam.out> <sam.in>

[fznajar]

Thanks all. It turned out my fasta reference sequence from illumina has a format problem as each sequences is one single long line. I just had to reformat it and it worked.

Thanks again for your help