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Old 09-30-2009, 04:22 PM   #1
MQ-BCBB
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Default how to convert BLAT output (pslx or maf) to gff, sam, wig to load in browser

I was able to view BLAT output (psl format) in the IGB (igb.bioviz.org) but would like to be able to use the BROAD IGV instead which doesn't recognize any of the BLAT outputs.

Is there a way to convert a psl, pslx, or maf format to sam, wig, gff or any other format that will allow me to view my sequences using IGV?

Thank you!
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Old 11-06-2009, 03:26 PM   #2
DrD2009
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I'm pretty new to the field of bioinformatics, but I have been dealing with a very similar situation, taking the PSL output of BLAT and putting it into a GFF file.

I've been processing the PSL files on Galaxy (http://main.g2.bx.psu.edu/). It pretty easy and only takes a minute to convert it over into a GFF.

Steps:
1.) Upload the PSL file and select the file type as tabular. (get data>upload file)
2.) Remove the header, if there is one (text manipulation>remove beginning). There are 5 lines in the header.
3.) Add columns for the source and feature fields. (text manipulation>add column)
4.) Add columns for the score, frame, and group (text manipulation>add column)
For these I just put "."
5.) Now that you have all the fields necessary for the GFF it is just a matter of cutting the columns in order. (text manipulation>cut).
6.) Click on the pencil to edit the name of the file and to change it into GFF format and the columns will be named with the proper GFF fields.

The first time it took me a while to figure out, but now I can go from PSL to GFF in about 1-2 minutes using Galaxy. There is probably an easy way to do it with programming and scripts, but this way has been working well for me.

Hope this helps.


-Brandon
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Old 11-16-2009, 07:48 AM   #3
MQ-BCBB
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Thanks for your reply. I haven't tried it but I will. I also found convenient to get to a sam output which could be sorted and indexed with the IGV tools and then displayed in the browser.
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Old 06-03-2010, 05:52 AM   #4
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Could you please describe the method you used to convert Blat to SAM?
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Old 06-03-2010, 10:50 AM   #5
rdeborja
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Default blat (psl) to sam

Samtools (v0.1.7) comes with a tool to convert psa to sam format called psl2sam.pl.
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Old 06-03-2010, 12:14 PM   #6
David
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We are trying to use Cufflinks to analyze our data. This requires CIGAR matching and it appears that psl2sam.py is unable to do this. Are there any other scripts or flags we can use for this particular application?
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Old 02-25-2011, 09:03 AM   #7
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Hi David - I would also like to use cufflinks to analyze BLAT aligned sequences. Did you find a solution to converting psl to sam with CIGAR matching?
Thanks!
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Old 11-22-2012, 10:13 AM   #8
pbarros
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Default how to convert BLAT output (pslx or maf) to gff, sam, wig to load in browser

Quote:
Originally Posted by rdeborja View Post
Samtools (v0.1.7) comes with a tool to convert psa to sam format called psl2sam.pl.
Dear all,
I've been trying to use this perl script (psl2sam.pl) to convert a .psl file (from BLAT).
However, this is not generating an output file (.sam)... instead, it just prints (what I think is) the output on shell

$path/psl2sam.pl myfile.psl

I'm not using any of the options in usage, but they are all related to the conversion itself and not about the output file...
I must add that I never used SAMtools before...
what am I missing here?

thank you in advance
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Old 11-23-2012, 08:13 AM   #9
pbarros
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Quote:
Originally Posted by pbarros View Post
Dear all,
I've been trying to use this perl script (psl2sam.pl) to convert a .psl file (from BLAT).
However, this is not generating an output file (.sam)... instead, it just prints (what I think is) the output on shell

$path/psl2sam.pl myfile.psl

I'm not using any of the options in usage, but they are all related to the conversion itself and not about the output file...
I must add that I never used SAMtools before...
what am I missing here?

thank you in advance
ok!
just found the answer for that!
never mind
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Old 11-24-2012, 06:23 PM   #10
Jim Robinson
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I'm pretty late to this thread, missed the original post. However, for the record IGV displays blat output in the form of .psl files, the extension must be .psl. There's no need to convert it to another format.

Jim
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Old 01-16-2013, 06:18 AM   #11
lechu502
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Hi, got to the same problem.
If you don't need mapping quality, I would get maf
(`blat -out=maf`) and then convert maf to sam (`maf-convert.py sam`) from last aligner last/src.
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Old 01-16-2013, 06:20 AM   #12
Jim Robinson
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Why don't you just load the blat output (.psl file)?
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