Multiple sam to bam followed by raw read count

Question

[Bioinfonext]

I have multiple sam file like this:

sam file location:

/data/SNU_work/Analysis/mapped/mapped

samtool location:

/home/yog/software/samtools-1.3.1/samtools

218_9W_Pa2.sam

218_9W_Pa1.sam

216_7W_Co1.sam

216_7W_Ca2.sam

216_7W_Ca1.sam

I converting them one by one using below commnad:

/home/yog/software/samtools-1.3.1/samtool view  -b 218_9W_Pa2.sam > 218_9W_Pa2.bam

After that I am extracting mapped read from bam file and sorting of bam using below cammnd:

 /home/yog/software/samtools-1.3.1/samtools view -b -F4 218_9W_Pa2.bam > 218_9W_Pa2.mapped.bam


/home/yog/software/samtools-1.3.1/samtools sort 218_9W_Pa2.mapped.bam -o 218_9W_Pa2_mapped_sort.bam

After sorting bam I also want to do index bam file and follwed by raw read count:

  For indexing: /home/yog/software/samtools-1.3.1/samtools index 218_9W_Pa2_mapped_sort.bam



 For read count: /home/yog/software/samtools-1.3.1/samtools idxstats 218_9W_Pa2_mapped_sort.bam > readcount_for_each_bam

Please, can you suggest how can I do all step for all sam files in a single command/scripts?

Thanks

Answer 1

[Istvan Albert]

You can add all your flags into a single command.

In addition, the latest samtools does not even need the -S flag as it detects the input type automatically.

samtools view -F 4 -b data.sam > data.bam

To run all of these commands on all SAM file you could automate with:

ls *.sam | xargs -n 1 -I {} sh -c 'samtools view -F 4 -b {} > {}.bam'

Annoyingly this will add another extension .sam.bam so you would need to also apply a batch rename (you can find many examples of that on StackOverflow).

A more elegant solution (and the recommended practice) would be to use GNU Parallel:

ls *.sam | parallel 'samtools view -F 4 -b {} > {.}.bam'

[Bioinfonext]

I removed flag -S from command as you have suggested.

[Bioinfonext]

I used this scripts and I able to extract mapped reads from sam file to in the bam format.

ls *.sam | xargs -n 1 -I {} sh -c 'samtools view -F 4 -b {} > {}.bam'

Now can you please suggest how to sort and index all these bam files?

[Istvan Albert]

replace the text within the single quotes with the command you wish to execute.

In general, when someone helps you with an advice you need to make a concerted effort to understand what the content consists of and how it works - that way it is easy to generalize and apply to a different situation.

[WouterDeCoster]

Conceptually quite easy is a for loop

for f in *.bam
do
samtools index $f
done

[CS]

to avoid .sam.bam you can do for j in *.sam ; do basename $j .sam ;done |sed ':a;N;$!ba;s/\n/ /g' sed is just removing the new lines by spaces

Answer 2

[badribio]

Look here this may help Using Samtools On Many Files Recursively In One Go

[Istvan Albert]

I would not recommend this post as it references an old version of samtools and the commands listed might not work anymore.

[badribio]

thank you for correcting ! I should have mentioned about version difference.