SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Color-space mapping with Bowtie ikarus97 Bioinformatics 3 06-30-2011 09:56 AM
EBI NGS Workshop 4th-6th April 2011: spaces still available cochrane Events / Conferences 0 03-19-2011 02:29 AM
Bowtie, Color-space reads, and confusing base qualities at variable sites keebs42 Bioinformatics 6 03-13-2010 05:51 PM
Bowtie and Color Space cutcopy11 SOLiD 9 02-05-2010 03:50 AM
direct mapping of color-space data against color-space begsch SOLiD 1 09-09-2009 10:25 PM

Reply
 
Thread Tools
Old 01-19-2010, 07:51 AM   #1
anusha
Junior Member
 
Location: Newark, New Jersey

Join Date: Jan 2010
Posts: 6
Default Bowtie -Color spaces

Hi i trying to work with bowtie on color spaces.
I got the csfasta and qual files from the SOLID and now need to run bowtie to analyse it. But bowtie reads the fastaq files.
Can anyone help me in getting the .fq files from csfasta and qual files.
The question may be silly but it is hard to me since i am beginner.

Thanks
Anu
anusha is offline   Reply With Quote
Old 01-19-2010, 09:00 AM   #2
kopi-o
Senior Member
 
Location: Stockholm, Sweden

Join Date: Feb 2008
Posts: 319
Default

I think the BFAST package contains a Perl script which will do that for you.
kopi-o is offline   Reply With Quote
Old 01-19-2010, 12:17 PM   #3
Chipper
Senior Member
 
Location: Sweden

Join Date: Mar 2008
Posts: 324
Default

http://bowtie-bio.sourceforge.net/ma...lorspace-reads

Have not tried the galaxy software but BFASTs solid2fastq (c-version) works well.
Chipper is offline   Reply With Quote
Old 01-19-2010, 12:24 PM   #4
anusha
Junior Member
 
Location: Newark, New Jersey

Join Date: Jan 2010
Posts: 6
Default

Thank you.I tried in galaxy but i am getting the output file as fastaqsanger.
I am now checking out whether i can use that in bowtie. If this doesnt work i wil try in BFAST's.
anusha is offline   Reply With Quote
Old 01-20-2010, 12:14 PM   #5
anusha
Junior Member
 
Location: Newark, New Jersey

Join Date: Jan 2010
Posts: 6
Default

Hi I tried and able to run in Bowtie but it shows a very low alignment. so i am trying to do comparison using maq. while i am running maq i got the following error message.

[anusha@njmscluster maq-0.7.1]$ ./maq csmap2nt aln.map aln.nt.map ref.bfa aln.cs.map
maq: csmap2ntmap.cc:163: int maq_csmap2nt(int, char**): Assertion `fpout && fpin && fp_bfa' failed.
Aborted

what i understood is there is a error in the csmap2nt.cc program which is inbuilt with the maq package.
If anyone know about help me out.

Thanks
Anu
anusha is offline   Reply With Quote
Old 01-20-2010, 10:03 PM   #6
Jonathan
Member
 
Location: Germany

Join Date: Jun 2009
Posts: 36
Default

No, the given command line is wrong (as can be seen when not giving any params):

./maq csmap2nt aln.map aln.nt.map ref.bfa aln.cs.map
should be
./maq csmap2nt aln.nt.map ref.bfa aln.cs.map

./maq csmap2nt states:
Usage: maq csmap2nt <out.nt.map> <in.ref.nt.bfa> <in.cs.map>

But likely you will have strange alignments - see my newly started thread here

Best
-Jonathan
Jonathan is offline   Reply With Quote
Old 02-02-2010, 05:35 PM   #7
rdeborja
Member
 
Location: Toronto

Join Date: Aug 2008
Posts: 42
Default

solid2fastq has done the trick for me (C version). Here's some general stats on a few single tag runs I performed:
- full flowcell with ~400M reads
- csfastq files broken down to 20M reads / file
- alignment resulted in ~50% aligned reads
- total run time for job 13 minutes over 20 computer nodes with threads set to 8 (-p flag)
- comparable results to CoronaLite

Next up for us, matepair analysis followed by whole transcriptome.
rdeborja is offline   Reply With Quote
Old 02-03-2010, 06:05 AM   #8
idonaldson
Member
 
Location: Manchester, UK

Join Date: Oct 2009
Posts: 37
Default

I am trying Bowtie with SOLiD data and have achieved ~40% mapping efficiency for uniquely mapped (-m 1) reads. I am using the python script from Galaxy to create fastq files, see http://bitbucket.org/galaxy/galaxy-c...solid2fastq.py
idonaldson is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:05 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO