samtools psl2sam.pl usage?

[ehlin]

I have a .psl file generated from BLAT. I want to convert it to SAM so I can sort out relevant sequences. I tried using psl2sam.pl in SamTools but when I try to view I get:

[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

I didn't specify any parameters when I ran psl2sam.pl, and I have no idea what any of them mean. The usage says:

Usage: psl2sam.pl [-a 1] [-b 3] [-q 5] [-r 2] <in.psl>

I have no idea what this means, could anyone explain? Thanks.

[mgogol]

Well, usually that means a sam file is missing a header... I wonder if it wants one on the psl file, that seems weird. You can generate a header with:

samtools view -bt genome.fa.fai sample.sam
or
picard CreateSequenceDictionary

[kmcarr]

I have a .psl file generated from BLAT. I want to convert it to SAM so I can sort out relevant sequences. I tried using psl2sam.pl in SamTools but when I try to view I get:

[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!

I didn't specify any parameters when I ran psl2sam.pl, and I have no idea what any of them mean. The usage says:

Usage: psl2sam.pl [-a 1] [-b 3] [-q 5] [-r 2] <in.psl>

I have no idea what this means, could anyone explain? Thanks.

Could you please show exactly the command you used.

[freeseek]

Command line for psl2bam conversion

Assuming ref.fasta is the reference file used for alignment with blat and in.psl is the output of the blat alignment, these commands will generate the bam file from the blat alignments:

samtools faidx ref.fasta # if the reference is not already indexed
psl2sam.pl in.psl | samtools view -bt ref.fasta.fai -o out.bam -