Question: aligning multiple fasta files
1
gravatar for F
3.9 years ago by
F3.4k
Iran
F3.4k wrote:

hey biostars,

how i can align multiple fastq files on reference genome or i have to align them individually?? 

 

ADD COMMENTlink modified 3.9 years ago by verma30 • written 3.9 years ago by F3.4k
2
gravatar for RamRS
3.9 years ago by
RamRS21k
Houston, TX
RamRS21k wrote:

You can definitely align multiple FASTQ files to a reference genome - I do it all the time. You'd ideally be able to pass as parameters pairs of PE fastq files and any number of SE fastq files. Check out the documentation of the alignment program you're using to figure out the exact method to pass multiple files.

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by RamRS21k

thank you

ADD REPLYlink written 3.9 years ago by F3.4k
0
gravatar for vinay.baranwal
3.9 years ago by
India
vinay.baranwal0 wrote:

Use STAR aligner. It's very efficient provided you have the RAM resources.

ADD COMMENTlink written 3.9 years ago by vinay.baranwal0

thanks a lot

ADD REPLYlink written 3.9 years ago by F3.4k
0
gravatar for verma
3.9 years ago by
verma30
India
verma30 wrote:

Hey Hii Sarah,

                         There is a tool called fasta genome search or you can use blast there is a blast for searching a given database or sequence you can use that also.

 

ADD COMMENTlink written 3.9 years ago by verma30
1

I'm sorry, but how is this relevant to the question?

ADD REPLYlink written 3.9 years ago by RamRS21k

hey Ram, yes you all right i also did not give him.

ADD REPLYlink written 3.9 years ago by F3.4k

thank you

ADD REPLYlink written 3.9 years ago by F3.4k
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