fastp issue (trimming and read filtering tool)
Hello, has anyone used fastp? I used it for trimming metagenomic libraries , the issue is that I used as input a file with 40M sequences and the output was a file with 11M sequences.
the filtering results des not give detail of what happened with the removed sequences , although there is a report that details the removed reads given diverse filtering parameters (Q20, Q30, adapter trimming) but almost all the reads passes these filters (98% aprox).
So what do you think that happened with more of the half of the reads ?
https://www.dropbox.com/s/iefrzp62w0ap1f7/FPDEC2017_L1S1D05.html?dl=0
• 1,566 views
•
link
written
by
v.berriosfarias •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Ribo-seq: Should low-quality reads be filtered at FASTQ or BAM stage after fastp trimming?
written by Sammy •
-
Fastp Trimming for WGS
written by j.k3096 •
-
99.9999% of Q30 bases is normal?
written by Aki •
-
fastp - can I trim specific adapters only?
written by liorglic
-
Help with clumpify.sh
written by tamu.anand •
-
statistical question (different number of gene orthologs on database)
written by v.berriosfarias •
-
which sequence adapter trimming tool should i use for my illumina 101pb reads ?
written by v.berriosfarias •
-
de novo transcriptome
written by valopes •
-
Kmer content failed in FastQC analysis
written by josmantorres •
-
Tool: fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with …
written by chen
Perhaps you have adapter dimers (i.e. no inserts)? These would otherwise have good QC metrics (e.g Q scores).
People are not likely to click on Dropbox links. If you want to show extended data then perhaps use
pastebin.comto post excerpts.If you are willing to try an alternate tool out give
bbduk.sha try. A guide is available.