search

OpenGene / fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
MIT License
1.93k stars 333 forks source link

Most reads are not overlapping #109

Open juulluu21 opened 6 years ago

juulluu21 commented 6 years ago

Hi,

I have several paired end libraries. I have ran fastp on them. I am confused to see the non-overlapped reads. Would you please explain what is the case?

Thanks.

screen shot 2018-11-15 at 4 41 04 pm screen shot 2018-11-15 at 4 43 00 pm
sfchen commented 6 years ago

What sequencer did you use?

juulluu21 commented 6 years ago

Illumina.

juulluu21 commented 6 years ago

Any help???

sfchen commented 6 years ago

What's the insert size distribution measured by the BAM file?

juulluu21 commented 5 years ago

I actually don't have a BAM file. My reads are for metagenomics, and I am not mapping them against anything.

I sort of inherited the files from previous lab members. I am not sure if they were processed (such as adapter clipping) before. If that is the case, do you think my issues is happening due to that? Thanks.

gabeng commented 5 years ago

I noticed a similar issue when I had fastq files where the sorting was out of order. This happens e. g. when fastq are created from a bam file that is not sorted by read name. See e. g. the samtools fastq documentation.