wow! thank you so much!
• 0 views
•
link
Illumina sequencing data trimming help
Hi! I never posted here before but I wanted somebody's opinion. I did paired end Illumina sequencing on mosquito DNA and ran fastqc to check the quality of my reads before trimming and they appear to be really good quality. I am wondering if I would like to use trimmomatic what do I trim here? Do i need to remove the first 20 bp using headcrop? and the last few bp are also off do I trim those? And also my sequence length varies greatly from 35-151. Is that ok or am I supposed to do something about that? Do I need to run sliding window or leading/trailing or minlegth? How do I know which numbers to set for each parameter? My reverse read had one single over represented sequence (GGGGGGG....) do I also need to trim that out or leave it?
• 166 views
•
link
1 answer
Looks like you do not need to do trimming since the data appears to be pre-scanned and pre-trimmed. Reason for this is the plots you post above. Key observation there is the following.
And also my sequence length varies greatly from 35-151.
If the data was not pre-trimmed, every read would have been of identical length, in this case 151 bp.
As for the variable pattern seen at the beginning of the reads,
Do i need to remove the first 20 bp using headcrop?
that is likely due to the tagmentation reaction during library prep showing some sequence preference. A similar thing happens with "random" primed libraries ( https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/ ) If you were to align the data as is, the beginning of reads should align without issues.
For poly-G reads, those could be easily removed but they otherwise should not align (unless mosquito genome is known to contain such homopolymer stretches).
• 0 views
•
link
Log in to answer this question.