Question: BAM/SAM to FASTA conversion
3
gravatar for biolab
4.5 years ago by
biolab1.1k
biolab1.1k 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 • 32k views
ADD COMMENTlink modified 18 months ago by genomax70k • written 4.5 years ago by biolab1.1k
3
gravatar for Chadi Saad
2.1 years ago by
Chadi Saad60
France
Chadi Saad60 wrote:

you need to add '-' fot seqtk in order to read from pipe :

samtools bam2fq input.bam | seqtk seq -A - > output.fa
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Chadi Saad60

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

ADD REPLYlink written 2.1 years ago by WouterDeCoster40k
12
gravatar for Carambakaracho
18 months ago by
Carambakaracho1.5k
Switzerland/Basel
Carambakaracho1.5k 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 18 months ago by Carambakaracho1.5k
11
gravatar for Istvan Albert
4.5 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k 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The advice in the post you link to is greatly outdated.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 4.5 years ago • written 4.5 years ago by Istvan Albert ♦♦ 81k

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 4.5 years ago by biolab1.1k
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 4.5 years ago by Istvan Albert ♦♦ 81k

Hi Istvan, your answer is really helpful.

ADD REPLYlink written 4.5 years ago by biolab1.1k
2
gravatar for genomax
18 months ago by
genomax70k
United States
genomax70k 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 18 months ago • written 18 months ago by genomax70k
1
gravatar for Alex Reynolds
18 months ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k 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 18 months ago • written 18 months ago by Alex Reynolds28k

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 4 weeks ago by genomax70k • written 4 weeks ago by xiaoleiusc0

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 4 weeks ago by Alex Reynolds28k

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 4 weeks ago by xiaoleiusc0
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 29 days ago • written 4 weeks ago by Alex Reynolds28k
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