Convert Sam2Psl Or Sam2Axt?
I've googled for sam2psl and found a couple of references to it, but I actually think they are referring to psl2sam, other way around.
Has anybody got any idea if there is a sam2psl or sam2axt tool somewhere as part of a package or as a simple script?
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I have the same issue. I want to convert SAM/BAM file to BLAT PSL file format. I found the psl2sam in samtools. Has anyone found an answer to this? Please help.
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Is it possible to use awk?
Just curious, but what is it that you want to do with the psl-format file? Perhaps there is a tool that will do the same thing with SAM?
@Sean Davis: this is to run axtChain on the resulting file. Both psl or axt would do.
My guess is that you will have to write something yourself. In the end, it may be faster to simply realign with blat.
Could any of the following help: sam2hmmer, sam2psi, sam2vcf.pl?