Question: Aligning Multiple paired end files together
0
gravatar for David_emir
17 months ago by
David_emir370
India
David_emir370 wrote:

Hi All,

I have 72 paired end .fastq file for which i need to do Alignment using BWA. Since its a paired end data and my files are named as

  1. sam_001_1.fastq

  2. sam_001_2.fastq

  3. sam_002_1.fastq

  4. sam_002_2.fastq & so on

Since its a paired end data i am not able to generate a single .sam file using a shell script. my script is generating individual .sam file for each .fastq files. Please let me know whats the best strategy for handling this.

EDIT:1 My script

for i in *.fastq;

do

bwa mem -t 10 /data2/Exome/HG19/BWA/hg19 1.$i 2.$i > /data2/validation_samples/fastq2sam/$i.sam; 

done

Sincerely,

Dave

shell bwa alignment assembly • 1.4k views
ADD COMMENTlink modified 17 months ago • written 17 months ago by David_emir370

my script is generating individual .sam file for each .fastq files

Please show us this script.

Thanks!

fin swimmer

ADD REPLYlink written 17 months ago by finswimmer13k

Thanks for the reply, i have added my script, please have a look

ADD REPLYlink written 17 months ago by David_emir370

Did you tried to run this but except executing bwa, only do echo $i (just a tip)

ADD REPLYlink written 17 months ago by gb1.9k
1
gravatar for Joe
17 months ago by
Joe18k
United Kingdom
Joe18k wrote:

Your loop isnt working quite how you think it is. Each iteration of the loop is only operating on a single fastq file.

What you need to do is, loop over all the R1s, strip the filename down to its ‘base’, without the R1/R2, then reconstitute the second filename on the fly (or use file pairing with GNU parallel but I can’t find the link right now).

There are quite a few similar questions to this task on the forum, so there will be a pre-existing loop template you can try.

Edit: found the link:

A: Automating Trimmomatic for total Noobs

ADD COMMENTlink modified 17 months ago • written 17 months ago by Joe18k
1

Thanks a lot for your help, i am able to sucessfully run BWA on my .fastq files. with following code,

for f in $(ls *.fq_filtered | sed -e 's/_1.fq_filtered//' -e 's/_2.fq_filtered//' | sort -u)
do
bwa mem -t 20 hg19 ${f}_1.fq_filtered ${f}_2.fq_filtered > /path/to/be/saved/${f}.sam
done
ADD REPLYlink written 17 months ago by David_emir370
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