Question: Fasta File To Sam Conversion
1
gravatar for Rallapalli Sukeerthi Teja
8.2 years ago by

Hi,

Is it possible to convert a fasta file to sam/bam format using galaxy OR Sam tools in MAC ?

And how can i call SNP's using samtools. ?

OR

Is is possible to call SNP's using Blast 2.2.25 (Stand Alone Blast)

Thank you Teja

fasta format sam conversion • 12k views
ADD COMMENTlink modified 13 months ago by harishchander.a0 • written 8.2 years ago by Rallapalli Sukeerthi Teja10
2

Are you working on NGS data ? Do you have fastq files ? FASTA file is a simple format with a header and a sequence. For generating SAM format you need a FASTQ file see: samtools.sourceforge.net/SAM1.pdf For BAM format specifications: see section 3 of the same file.

ADD REPLYlink written 8.2 years ago by Khader Shameer18k

When I use "reformat.sh in=your.fa out=your.sam". I am geting the error as "Error: Could not find or load main class jgi.ReformatReads". Please help me to rectify this error. Thanks in advance.

ADD REPLYlink written 13 months ago by harishchander.a0

Are you running this on windows? If so you will need to run

java -cp /path/to/current jgi.ReformatReads in=reads.fq out=mapped.sam

...where /path/to/current is the location of the 'current' directory.

ADD REPLYlink written 13 months ago by genomax69k
8
gravatar for Istvan Albert
8.2 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

FASTA is a sequence representation format, SAM is a sequence alignment format, it makes little sense to transform a FASTA to SAM format, it would mean that all the aligment columns would be empty.

I suspect your intent is different.

ADD COMMENTlink written 8.2 years ago by Istvan Albert ♦♦ 80k
1

Istvan Albert and yet here I am looking for a solution. Also large sequencing centers are now delivering unaligned bam files. It's not sane, but so it goes.

ADD REPLYlink written 2.4 years ago by Zev.Kronenberg11k
2

Since you asked: reformat.sh from BBMap. reformat.sh in=your.fa out=your.sam (if you have samtools available in PATH, then you could write bam files directly).

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax69k
4
gravatar for Rrr
7.4 years ago by
Rrr40
Rrr40 wrote:

"FASTA is a sequence representation format"

FASTA is used both for unaligned and aligned sequence representation.

ADD COMMENTlink written 7.4 years ago by Rrr40

Wasn't the FASTA format derived from the FAST-A (FAST-P) alignment algorithm?

ADD REPLYlink written 16 months ago by mrals8930

See this thread for an interesting historical perspective by Bill Pearson on Fasta: Was FASTA ever popular?

ADD REPLYlink written 16 months ago by genomax69k
2
gravatar for Michael Dondrup
8.2 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

Is it possible to convert a fasta file to sam/bam format using galaxy OR Sam tools in MAC ?

No, (or if so that makes little sense, see Istvan's answer) but you can run an alignment program to align the sequences to a reference sequence. e.g. blat (to convert blat output see here), lastz or SHRiMP. This has been also answered here.

And how can i call SNP's using samtools. ?

samtools mpileup

and look here

Is is possible to call SNP's using Blast 2.2.25 (Stand Alone Blast)

No, that makes no sense to me.

ADD COMMENTlink modified 8.2 years ago • written 8.2 years ago by Michael Dondrup46k
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