Hi Antonio Thanks for the reply and I must say that you are right in your suggestion. Somehow my .psl file was changed in course of following the steps. I am sorry for that. Now, I am getting the results that I was looking for. Thanks a lot and best regards. Fahim
On Tue, Jun 29, 2010 at 12:52 AM, Antonio Coelho <[email protected]>wrote: > Hello Fahim, > I would suggest ensuring that your transformations of the files > didn't accidentally change them to not follow PSL format rules. A clean > concatenation should leave you with a working PSL file. If you find that > this isn't the case, please send us your error message (along with some > sample lines from your file if you feel comfortable doing that) so we > can have a better sense of what might be wrong. > > I hope this helps. Please contact us again if your problems persists, or > if you have other inquiries. > > Best > Antonio Coelho > UCSC Genome Bioinformatics Group > > > ----- Original Message ----- > From: "Fahim Md" <[email protected]> > To: [email protected], [email protected] > Sent: Monday, June 28, 2010 2:26:22 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] pslReps help > > I am using pslReps executable which I downloaded as part of pslUtils from > Kent's website for analyzing repeats and generating genome wide best > alignments. > Since the size of psl files are huge, I generated those psl files with > -noHead option and then used sort in linux to generate a single file which > is now in tab delimited format > Now, I want to apply pslReps function on this file. since pslReps are not > in > psl format, it is giving me error. Is there any way through which I can > use > pslReps on this file. > Thanks and regards. > > -Fahim > Bioinformatics Lab > University of Louisville > Louisville, KY - 40217 > 502-409-1167 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > -- Fahim Mohammad Bioinforformatics Lab University of Louisville Louisville, KY, USA Ph: +1-502-409-1167 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
