Question: How to convert fastq file with raw reads to draft genome fastq file ?
0
gravatar for gskbioinfo143
18 months ago by
India
gskbioinfo14350 wrote:

Hi sir/mam,

i have done mapping of Streptococcus pneumonia raw sequenced data with reference Streptococcus pneumonia ATCC 700669 using bowtie2. i have converted from .bam file to .fasta file. the fasta file it has the raw reads - that is the fasta file just stripped of the quality scores know how to get draft genome fasta file.

fasta read image https://ibb.co/cMDzRQ

Need help

thanks

fastq • 704 views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 18 months ago by gskbioinfo14350
2

It sounds like you are trying to assemble a library. In that case, I'd suggest preprocessing the data to clean it up, then assembling it with Spades to yield a draft genome. Mapping to a related genome is not usually part of this process unless you are trying to reduce contamination or you want to do a reference-guided assembly.

ADD REPLYlink modified 18 months ago • written 18 months ago by Brian Bushnell16k

Yes sir, im actually looking for reference based mapping of reads

ADD REPLYlink written 18 months ago by gskbioinfo14350
1

not sure what you mean by "how to get draft genome fasta file", please explain better.

ADD REPLYlink written 18 months ago by Michael Dondrup45k

You have to make an assembly "assembling", not mapping, if your reference is a very conserved specie you can make a guided assembly using spades, idba-hybrid or trinity, if it doesn´t, you have to make a "denovo" assembly in which case I would recommend you spades.

ADD REPLYlink written 18 months ago by Buffo1.2k

http://spades.bioinf.spbau.ru/release3.10.1/manual.html

we cant do reference based mapping (assembly) with spades as given in spades manuel

thanks need your suggestions

ADD REPLYlink written 18 months ago by gskbioinfo14350
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