Question: How can I only took the mapped ones from STAR ?
0
gravatar for rekren
4 days ago by
rekren0
rekren0 wrote:

Hello,

I wanted to obtain only the "mapped" reads as an output of the STAR. I forgot to delete "--outSAMunmapped Within " and all of my mapped output files also contain all unmapped reads,too. Data size is huge and re-mapping properly wiil take so much time...

How can I fix the BAM files which were supposed to be mapped reads but also include unmapped reads in it ?

#!/bin/bash
mkdir /mnt/data/Toxo_scan/GBR_Male/ToxoMap
while read -r line
do
mkdir ToxoMap/$line
echo $line" -> Running STAR - Toxo now"
STAR  --runThreadN 12 --alignIntronMax 1 --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --genomeDir "/mnt/data/Toxo_scan/toxo_genome" --readFilesIn "/mnt/data/Toxo_scan/GBR_Male/sickle/"$line"_1_clean.fastq" "/mnt/data/Toxo_scan/GBR_Male/sickle/"$line"_2_clean.fastq" --outFileNamePrefix "/mnt/data/Toxo_scan/GBR_Male/ToxoMap/"$line"_" --outReadsUnmapped Fastx
done
ADD COMMENTlink modified 4 days ago by andrew.j.skelton733.1k • written 4 days ago by rekren0

Is the presence of unmapped reads causing issues? If you were going to do counts etc those reads will be ignored.

ADD REPLYlink written 4 days ago by genomax226k

They were causing the issues because, I was supposed to process only the mapped reads in the workflow. For my case, presence of the unmapped reads in the mapped reads is like having false positive results into the true positive results...

ADD REPLYlink written 4 days ago by rekren0
1

Out of curiosity what was the downstream workflow component that was causing a problem? Most programs should understand reads that are unmapped easily.

ADD REPLYlink modified 4 days ago • written 4 days ago by genomax226k

The issue was not related with downstream workflow components, it was about my supervisor's satisfaction :) When I came with millions of undesired "unmapped" reads as a result of "mapped" reads, I was in the position of not doing the task well. That's all :)

ADD REPLYlink written 4 days ago by rekren0

it was about my supervisor's satisfaction :)

Aha. No logical solution would suffice in that case.

ADD REPLYlink written 4 days ago by genomax226k
3
gravatar for andrew.j.skelton73
4 days ago by
Newcastle Upon Tyne
andrew.j.skelton733.1k wrote:

To get your mapped reads:

samtools view -b -F 4 alignment.bam > mapped.bam

To get your unmapped reads:

samtools view -b -f 4 alignment.bam > unmapped.bam

The -f filters based on bitwise samflags. Flag 4 (or 0x0004) is for unmapped reads. -F does the inverse.

ADD COMMENTlink written 4 days ago by andrew.j.skelton733.1k

Thanks a lot friend, it worked.

ADD REPLYlink written 4 days ago by rekren0
1

Go ahead and accept the answer (green checkmark) to provide closure to the thread. You can accept more than one answer.

ADD REPLYlink written 4 days ago by genomax226k
3
gravatar for Macspider
4 days ago by
Macspider930
Vienna - BOKU
Macspider930 wrote:

This is what you're looking for:

samtools view -f 0x2 foo.bam > foo.filtered.bam

It will keep only the proper pairs in your alignment (if paired end). Proper pairs: correct orientation and within insert size.

ADD COMMENTlink written 4 days ago by Macspider930
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