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Old 10-28-2009, 04:40 AM   #1
idonaldson
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Default SHRiMP - how to obtain unique mapped reads?

Hi,

Can any SHRiMP users tell me how they obtain unique mapped reads (those mapped reads that only map to one position in the genome). I am mapping 50bp reads to the human genome. I have run rmapper-cs using the 'fast' and '50bp' settings.

Thanks!

Ian
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Old 11-03-2009, 01:28 AM   #2
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Default nudge

nudge for second viewing, thanks!
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Old 11-03-2009, 02:24 AM   #3
nilshomer
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Originally Posted by idonaldson View Post
nudge for second viewing, thanks!
You will need to write your own post-alignment filtering script. You can bug the authors to get the output to SAM format, which would make things easier.
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Old 11-04-2009, 03:32 AM   #4
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Default SHRiMP now can output in SAM

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Originally Posted by nilshomer View Post
You will need to write your own post-alignment filtering script. You can bug the authors to get the output to SAM format, which would make things easier.
The latest 6 Oct (V1.30) version has a shrimp2sam.pl script in the /Utils folder.
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Old 11-05-2009, 09:33 PM   #5
Torst
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Quote:
Originally Posted by idonaldson View Post
Hi,
Can any SHRiMP users tell me how they obtain unique mapped reads (those mapped reads that only map to one position in the genome). I am mapping 50bp reads to the human genome. I have run rmapper-cs using the 'fast' and '50bp' settings.
This perl code will take 'hits.txt' on stdin and write 'unique_hits.txt' on stdout.

Code:
#!/usr/bin/perl -w
my %seen;
while (my $line = <>) {
  my @f = split m/\t/, $line;
  next unless @f == 10;
  next if $seen{ $f[0] }++;
  print $line;
}
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Old 11-10-2009, 02:33 AM   #6
idonaldson
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Thanks for your input!
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Old 11-10-2009, 02:49 PM   #7
sci_guy
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Originally Posted by nilshomer View Post
You will need to write your own post-alignment filtering script. You can bug the authors to get the output to SAM format, which would make things easier.
@Nils; I am amused The SAM munging Perl script in the 1.3.0 SHRiMP distribution is actually one authored by you.
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Old 11-10-2009, 07:38 PM   #8
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@Nils; I am amused The SAM munging Perl script in the 1.3.0 SHRiMP distribution is actually one authored by you.
I wrote it to compare aligners a while ago for a paper that is being published tomorrow (yay). Needless to say, I have done a lot of aligner comparisons.

Unfortunately the SHRiMP to SAM script does not support paired end reads...
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Old 06-03-2010, 11:51 AM   #9
ulisses de padua
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I do rmmaper -cs and I am using sensitive 50bp...
my dates are mate pair, and I do it for _F3 file and for _R3file... The results are in two
different folders.

I am using Shrimp 1.3.2....

How I obtain the unique file for run the probcalc?


I would like to receive a answer by my personal email too: email: upadua@yahoo.com.br

Thanks regards

Last edited by ulisses de padua; 06-06-2010 at 04:02 PM. Reason: Shrimp version
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Old 06-28-2010, 09:13 AM   #10
rahul.m.dhodapkar
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I am trying to run SHRiMP2 on paired-end data. I have run the indexing step, and am using

./gmapper-ls /Test_seq/test.fa -L hg18_combined.fa -V -N 8 -p opp-in >/Out_seq/shrimptestoutput

as my command. The index loads fine, and the reads file also loads, but then SHRiMP doesn't actually run and i get 0 mappings. Does anyone know how to fix this problem?

Many thanks.
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Old 07-02-2010, 03:48 PM   #11
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Hi Rahul,
I believe the command you wish to run is,
./gmapper-ls -L hg18_combined.fa -V -N 8 -p opp-in /Test_seq/test.fa >/Out_seq/shrimptestoutput
If you wish to have SAM output you can use,
./gmapper-ls -E -L hg18_combined.fa -V -N 8 -p opp-in /Test_seq/test.fa >/Out_seq/shrimptestoutput
If you wish to output the unaligned reads in SAM format or into a separate file, please email me (misko@cs.toronto.edu) and i can supply you with the unreleased version that supports this feature!

Misko
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