Bowtie -Color spaces

[anusha]

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

[kopi-o]

I think the BFAST package contains a Perl script which will do that for you.

[Chipper]

http://bowtie-bio.sourceforge.net/manual.shtml#colorspace-reads

Have not tried the galaxy software but BFASTs solid2fastq (c-version) works well.

[anusha]

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]

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

[Jonathan]

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

[rdeborja]

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.

[idonaldson]

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