It is weird there are no reads less than 100 bp in qualimap.

Question

[Dan]

For ATAC-seq, I trimmed the reads using

trim_galore --illumina --paired --fastqc \ 
fastq/${FILE}/*R1_001.fastq.gz fastq/${FILE}/*R2_001.fastq.gz \
-o trim/${FILE}

When I run Bowtie2 using

bowtie2 --local --very-sensitive-local --no-mixed --no-discordant \
-x Bowtie2_index/mm10/mm10 \
-1 trim/${FILE}/*val_1.fq.gz \
-2 trim/${FILE}/*val_2.fq.gz \
| samtools view -Sb | samtools sort > Bowtie2_output/${FILE}_sort.bam

and qualimap qualimap bamqc -bam, It is weird there are no reads less than 100 bp. There should be less than 100 bp reads I think. Can anyone tell me what is wrong?

Thanks a lot.

Answer 1

[Dan]

I tried bamsormadup combined with bowtie2

bowtie2 --local --very-sensitive-local --no-mixed --no-discordant -p 24 \
-x /lila/data/chen/dan/Bowtie2_index/mm10/mm10 \
-1 trim/${FILE}/*val_1.fq.gz \
-2 trim/${FILE}/*val_2.fq.gz \
| bamsormadup inputformat=sam threads=24 SO=coordinate outputformat=bam \
indexfilename=bam/${FILE}"_mm10.bam.bai" > bam/${FILE}"_mm10.bam"

Now the reads length are correct

Answer 2

[Trivas]

This sounds like a problem with TrimGalore. The default functionality is to remove reads or read pairs where the length of the sequence after trimming is 20 nt or shorter. Try adding --length 0 to turn this feature off and see if that corrects anything.