Aligning Multiple paired end files together

Question

[David_emir]

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

[DareDevil]

the logic to be applied is mentioned here

[finswimmer]

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

Please show us this script.

Thanks!

fin swimmer

[David_emir]

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

[gb]

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

Answer 1

[Joe]

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

[David_emir]

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

[etoketim]

Awesome @David_emir! To get my bam files direct I simply replaced

/path/to/be/saved/${f}.sam]

with

l samtools sort -o ${f}.bam