Automated script for paired end sequencing

[Alex852013]

Hello everybody,

I have a folder with paired end sequencing data (divided by the asterisk to make group clearly visible here). I would like to run an automated script, which analyses couple by couple (trimming, mapping and so one). I already introduced placeholders for the single steps, but I don't know how to introduce two file (which belong together) at the same time.
I would be thankful, if someone had a hint for me.

10pct-0_S3_R1_001.fastq
10pct-0_S3_R2_001.fastq
*
10pct-0_S7_R1_001.fastq
10pct-0_S7_R2_001.fastq
*
10pct-15_S4_R1_001.fastq
10pct-15_S4_R2_001.fastq
*
10pct-15_S8_R1_001.fastq
10pct-15_S8_R2_001.fastq



placeholder1='name1'
placeholder2='name2'
placeholder3='beginning_of_the_couple_name'

for placeholder1 in *; do

trim_galore ../$placeholder1.fastq ../$placeholder2.fastq -q 20 --paired --phred33
bowtie2 $bowtie_opts $bowtie_index -1 ../$placeholder1.fq -2 ../$placeholder2.fq > $placeholder3.SAM


samtools view -bS ../$placeholder3.SAM > $placeholder3.BAM

samtools sort $placeholder3.BAM Sorted_BAMs/sorted_$placeholder3

…

done

[azneto]

You don't need to get both names. Just take the first one use regex to change the _R1_ part or get rid of everything from _R1_

Try this:

placeholder1='name1'
placeholder2=`echo $placeholder1 | sed 's/_R1_/_R2_/g'`
placeholder3=`echo $placeholder1 | sed 's/_R1_\S\+//g'`

[Alex852013]

Thanks a lot for the quick reply!
Now i run into the trouble, that i only need to choose every 2nd file.
I wanted to start by listing all files ending with fastq and putting them into a variable, but this files=*.fastq only returns the first file

[azneto]

Rather than:

placeholder1='name1'
placeholder2='name2'
placeholder3='beginning_of_the_couple_name'

for placeholder1 in *; do

try:


for placeholder1 in `ls *_R1_*.fastq`; do

placeholder2=`echo $placeholder1 | sed 's/_R1_/_R2_/g'`
placeholder3=`echo $placeholder1 | sed 's/_R1_\S\+//g'`

[Alex852013]

So this will start with this file:
10pct-0_S3_R1_001.fastq
use it as placeholder and also use this file for the second placeholder:
->10pct-0_S3_R2_001.fastq<-
Nevertheless, as soon as the first round is finished, it will start over with this file again:
->10pct-0_S3_R2_001.fastq<-
I would need something to skip this file.
Everything i tried so far totally fails...

[azneto]

I've noticed that and changed my reply. Check it out:

for placeholder1 in `ls *_R1_*.fastq`; do

[Alex852013]

Thanks a lot!
Sorry, i didn't see that you changed your post.
This solution is not what i thought of, but it's easy and solves the problem
Thank you.