Question: BAM/SAM to FASTA conversion
3
gravatar for biolab
5.0 years ago by
biolab1.2k
biolab1.2k wrote:

Hi everone,

I searched Biostars for BAM/SAM to FASTA conversion method, and found the tools EMBOSS Picard could do this (Convert Bam File To Fasta File)   I am wondering is there any perl script to complish this work?   I should note that my seq data is strand-specific seq, so the command samtools view filename.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' may not be very good.

I appreciate any of your solutions. Thanks a lot!

sam bam • 37k views
ADD COMMENTlink modified 2.0 years ago by genomax78k • written 5.0 years ago by biolab1.2k
15
gravatar for Carambakaracho
2.0 years ago by
Carambakaracho2.0k
Germany/Cologne
Carambakaracho2.0k wrote:

For future record: samtools versions >1.3 can convert bam to fasta directly via samtools fasta

samtools --help

Program: samtools (Tools for alignments in the SAM format)
Version: 1.4 (using htslib 1.4)

Usage:   samtools <command> [options]

Commands:
  [...]
  -- File operations
     [...]
     fastq          converts a BAM to a FASTQ
     fasta          converts a BAM to a FASTA
  [...]
ADD COMMENTlink written 2.0 years ago by Carambakaracho2.0k
12
gravatar for Istvan Albert
5.0 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

The advice in the post you link to is greatly outdated. One of the reasons we should revisit these posts. There are far easier/faster ways to accomplish the same task.

The latest versions of samtools have the bam2fq command. Chain that to seqtk seq like so:

samtools bam2fq input.bam | seqtk seq -A > output.fa
ADD COMMENTlink modified 5 months ago by RamRS25k • written 5.0 years ago by Istvan Albert ♦♦ 82k

Hi Istvan, thank you very much for your answer.  It's much helpful for my work.  I just have two more minor questions: (1) my samtools version is Version: 0.1.8 (r613).  I did not see samtools bam2fq function, so I need to update samtools?  (2) Additionally is seqtk inside samtools? If not, where to get it?  Thanks a lot!

ADD REPLYlink written 5.0 years ago by biolab1.2k
2

You need to update samtools to at least 1.1 http://www.htslib.org/

Get seqtk from https://github.com/lh3/seqtk see also  How To Obtain And Install Seqtk

ADD REPLYlink written 5.0 years ago by Istvan Albert ♦♦ 82k

Hi Istvan, your answer is really helpful.

ADD REPLYlink written 5.0 years ago by biolab1.2k
4
gravatar for Chadi Saad
2.6 years ago by
Chadi Saad70
France
Chadi Saad70 wrote:

You need to add '-' for seqtk in order to read from stdin :

samtools bam2fq input.bam | seqtk seq -A - > output.fa
ADD COMMENTlink modified 4 weeks ago by ATpoint29k • written 2.6 years ago by Chadi Saad70

You can add - but it is not necessary.

ADD REPLYlink written 4 weeks ago by ATpoint29k
2
gravatar for genomax
2.0 years ago by
genomax78k
United States
genomax78k wrote:

reformat.sh from BBMap suite will do the conversion efficiently.

reformat.sh in=your.bam out=seq.fa
reformat.sh in=your.sam out=seq.fa
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by genomax78k
1
gravatar for Alex Reynolds
2.0 years ago by
Alex Reynolds29k
Seattle, WA USA
Alex Reynolds29k wrote:

Via bam2bed and bed2faidxsta.pl:

$ bam2bed < reads.bam | bed2faidxsta.pl > reads.fa

Or sam2bed:

$ sam2bed < reads.sam | bed2faidxsta.pl > reads.fa
ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Alex Reynolds29k

I followed your instruction and even copied the unzipped bed2faidxstal.pl to the target folder, I got error "(base) bieniaszs-ipro:K20 bieniaszlab$ sam2bed < NL43_5562_filterredreads_header.sam | bed2faidxsta.pl > NL43_5562_filterredreads_header.fa -bash: bed2faidxsta.pl: command not found".

Then I add "perl" before the bed2faidxstal.pl, I still got error as below:

(base) bieniaszs-ipro:K20 bieniaszlab$ sam2bed < NL43_5562_filterredreads_header.sam | perl bed2faidxsta.pl > NL43_5562_filterredreads_header.fa
[E::fai_build3_core] Failed to open the file /Users/bieniaszlab/miniconda3/data/K_SRF11_U/K_20/K20/NL43_WT_CLIP.fa.gz
[faidx] Could not load fai index of /Users/bieniaszlab/miniconda3/data/K_SRF11_U/K_20/K20/NL43_WT_CLIP.fa.gz
[E::fai_build3_core] Failed to open the file /Users/bieniaszlab/miniconda3/data/K_SRF11_U/K_20/K20/NL43_WT_CLIP.fa.gz
[faidx] Could not load fai index of /Users/bieniaszlab/miniconda3/data/K_SRF11_U/K_20/K20/NL43_WT_CLIP.fa.gz
[E::fai_build3_core] Failed to open the file /Users/bieniaszlab/miniconda3/data/K_SRF11_U/K_20/K20/NL43_WT_CLIP.fa.gz
[faidx] Could not load fai index of /Users/bieniaszlab/miniconda3/data/K_SRF11_U/K_20/K20/NL43_WT_CLIP.fa.gz
[E::fai_build3_core] Failed to open the file /Users/bieniaszlab/miniconda3/data/K_SRF11_U/K_20/K20/NL43_WT_CLIP.fa.gz
ADD REPLYlink modified 6 months ago by genomax78k • written 7 months ago by xiaoleiusc20

Put the directory containing the Perl script into your environment PATH, or run it with Perl. Make sure your FASTA is indexed with samtools.

ADD REPLYlink written 7 months ago by Alex Reynolds29k

Thanks. I need FASTA output from SAM input, you mean to make sure my SAM file (not FASTA file) is indexed right?

ADD REPLYlink written 7 months ago by xiaoleiusc20
1

No, I mean that your reference genome FASTA must be indexed, in order to get out FASTA based on the BED coords that come out of the SAM conversion step. (Sorry for brevity, I was on a cell phone. Feel free to follow up if this isn't clear.)

ADD REPLYlink modified 6 months ago • written 7 months ago by Alex Reynolds29k
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