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Old 11-16-2009, 02:57 AM   #1
shailesh
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Default about next generation sequencing

i have next generation sequencing data.
i want to analyse that, but the problum is we have reads in different format rather then the FASTA. so please suggest me a software which will convert all formats into FASTA format.

SHAILESH KUMAR
Research Scholar(JRF)
Dr.G.P.S.Raghava's group
Bioinformatics centre
Institute of Microbial Technology
Chandigarh, India 160036
Phone +919501214248
e-mail-shailesh@imtech.res.in
shailesh.97@gmail.com
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Old 11-16-2009, 11:12 AM   #2
nilshomer
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Quote:
Originally Posted by shailesh View Post
i have next generation sequencing data.
i want to analyse that, but the problum is we have reads in different format rather then the FASTA. so please suggest me a software which will convert all formats into FASTA format.

SHAILESH KUMAR
Research Scholar(JRF)
Dr.G.P.S.Raghava's group
Bioinformatics centre
Institute of Microbial Technology
Chandigarh, India 160036
Phone +919501214248
e-mail-shailesh@imtech.res.in
shailesh.97@gmail.com
In what format are your reads? What platform are you using? What analysis tool(s) are you going to use (i.e. some take FASTQ not FASTA)?
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Old 11-16-2009, 09:49 PM   #3
shailesh
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Default about data

This is the link for the gossypium raw reads. They also have the quality control files available at this site. This is the complete genome sequence of Gossypium raimondii, which is a diploid variety of cotton.
ftp://ftp.ncbi.nih.gov/pub/TraceDB/gossypium_raimondii/

I am not sure(as i havnt done any sequencing) about the plateform used, but it seems that this is a data from 454 SEQUENCER.
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Old 11-22-2009, 12:23 PM   #4
vadim
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Trace archive has compressed (gzip) fasta, look for files with names staring with 'fasta'.
For gossypium:
fasta.gossypium_raimondii.001.gz
fasta.gossypium_raimondii.002.gz
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Old 12-23-2009, 06:46 PM   #5
shailesh
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what is genome coverage and genome coverage depth..
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Old 12-27-2009, 08:12 PM   #6
shailesh
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I used velvet software for assembly of illumina reads,
Could you please tell me what will be the final result of this software ?
Is it lastgraph, graph or contig file? I could not understand what we have to do next after geting these files in the output?
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Old 12-27-2009, 10:01 PM   #7
ECO
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shailesh,

Please post in the correct forum. I'm not going to try to move every post to its proper place, so please make a new thread for your questions, or try searching the forums.
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Old 12-27-2009, 10:03 PM   #8
shailesh
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ok, I understand.
Thank you
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