Question: How Do You Convert A Sam/Bam File To A Psl Or Axt Format?
2
gravatar for lp364
6.2 years ago by
lp36420
lp36420 wrote:

I am trying to make a chain file to use in liftOver and these can be made using PSL or AXT files. My current data is in SAM/BAM. What's the best way to convert this to a psl or axt format?

samtools conversion • 2.7k views
ADD COMMENTlink modified 6.2 years ago by Alex Reynolds29k • written 6.2 years ago by lp36420

cross posted on seqanswers: http://seqanswers.com/forums/showthread.php?p=112080#post112080

ADD REPLYlink written 6.2 years ago by Pierre Lindenbaum123k
0
gravatar for Alex Reynolds
6.2 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

Perhaps you could try passing the output from the sam2bed script to the bed2psl.py script. I'd take care to make sure coordinate indexing is correct at each step of the process.

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Alex Reynolds29k
2

where can you download the bed2psl.py? It seems that the sam2bed doesn't process the cigar string that is needed to generate the psl.

ADD REPLYlink written 6.2 years ago by lenore.pipes20
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