script bash for counting

Question

[dorra.fass]

Hello,

I'm a beginner in writing script bash. I need your help to execute the featurecounts command for counting purposes for 10 mapped files corresponding to 10 samples located in 10 different directories. Please help me to get a right script. bash start code

#!/bin/bash

SOURCE_DIR_1=$/scratch/mapping_results/1
SOURCE_DIR_2=$/scratch/mapping_results/2
SOURCE_DIR_3=$/scratch/mapping_results/3
SOURCE_DIR_4=$/scratch/mapping_results/4
SOURCE_DIR_5=$/scratch/mapping_results/5
SOURCE_DIR_6=$/scratch/mapping_results/6
SOURCE_DIR_7=$/scratch/mapping_results/7
SOURCE_DIR_8=$/scratch/mapping_results/8
SOURCE_DIR_9=$/scratch/mapping_results/9
SOURCE_DIR_10=$/scratch/mapping_results/10

TARGET_DIR=$/scratch/counting

echo 'Going to $SOURCE_DIR'
cd $SOURCE_DIR

FILE_ARRAY=/$(locate Alignment.sam)

for file in $FILE_ARRAY; do
  featureCounts -t $SOURCE_DIR/$file -a /scratch/human/hg19.gtf -o $TARGET_DIR$....
  done

[cpad0112]

If you want to write counts for each sam file, into corresponding count file:

$ for i in $(seq 1 10); do
echo featureCounts -t "/scratch/mapping_results/$i/Alignment.sam" -a /scratch/human/hg19.gtf -o "/scratch/counting/$i.txt";
done

featureCounts -t /scratch/mapping_results/1/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/1.txt
featureCounts -t /scratch/mapping_results/2/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/2.txt
featureCounts -t /scratch/mapping_results/3/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/3.txt
featureCounts -t /scratch/mapping_results/4/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/4.txt
featureCounts -t /scratch/mapping_results/5/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/5.txt
featureCounts -t /scratch/mapping_results/6/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/6.txt
featureCounts -t /scratch/mapping_results/7/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/7.txt
featureCounts -t /scratch/mapping_results/8/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/8.txt
featureCounts -t /scratch/mapping_results/9/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/9.txt
featureCounts -t /scratch/mapping_results/10/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/10.txt

.

parallel --dry-run featureCounts -t /scratch/mapping_results/{}/Alignment.sam -a /scratch/human/hg19.gtf -o /scratch/counting/{}.txt ::: $(seq 1 10)

Probably you would not need a loop, as featurecounts writes each sample in a separate column. For all the samples (.sam), you can generate one single counts files where in each sample is represented one column with sample name.

[dorra.fass]

thank you so much for your help the script was executed with success

[dorra.fass]

Dear all,

Thank you so much for your responses and for your help I tried the following script

#!/bin/bash

SOURCE_DIR=/scratch/mapping_results/
TARGET_DIR=/scratch/counting

for SUBDIR in $(seq 1 10); do
featureCounts -t "$SOURCE_DIR/$SUBDIR/Alignment.sam" -a /scratch/human/hg19.gtf -o "$TARGET_DIR$"
done

Unfortunaltely i obtained only the counting results of sample 10 not all the samples. What can i do to resolve this problem in order to obtain counting results for each sample? Thanks a lot

[JC]

How many samples do you have? Are all /scratch/mapping_results/NN? The example only listed 1-10 ...

Answer 1

[JC]

#!/bin/bash

SOURCE_DIR=/scratch/mapping_results/
TARGET_DIR=/scratch/counting

for SUBDIR in $(seq 1 10); do
  featureCounts -t "$SOURCE_DIR/$SUBDIR/Alignment.sam" -a /scratch/human/hg19.gtf -o "$TARGET_DIR/$...".
done

Check https://www.gnu.org/software/bash/manual/

Answer 2

[young_bioinformatician]

I think, It would be like this:

for i in /scratch/mapping_results*
do 
    cd $i
    #optional; use echo pwd and check the where you are
    x=$(pwd)
    echo $(pwd)   
    featureCounts -t alignment.sam (or $x/alignment.sam) /scratch/human/hg19.gtf -o $TARGET_DIR$
    cd ../
done