Hi all friends,
For trimming polyA tail from RNA-seq data using bbduk, I found two flags:
"trimpolya=10”
, which trim leading or trailing sequences of at least 10 A or T and “literal=AAAAA”
along with adjusting the value of k= as needed.
I tried “trimpolya=10
”, but faced the error, seemingly, this flag is not known for the software. Regarding the second flag, “literal=AAAAA”, I’m in a doubt a bit if it should be “literal=TTTT
”, or not, please kindly clear me. Could you please also tell me what is your suggestion for k value for this trimming?
Thank you
Thanks. Sorry, how to find out which strand was sequenced? data obtained by Illumina TruSeq™ RNA Sample Preparation Kit. I just see a part of sequencing reads and don't see AAAA or TTT. However, mRNA was purified from total RNA using poly-T oligo-linked magnetic beads, so there is a probable AAA/TTT contamination. Would you please tell me what is the difference between two commands,
trimpolya=N
andliteral=TTTT
? However, after tryingtrimpolya=N
, the below error appeared:Could you please help me out with this issue?
Best,
Any suggestions, please!
I must have missed your last post. You are using a fairly old version of BBMap. So I suggest that you upgrade to the latest first.
With
trimpoly=
you need to replaceN
with a number you want. Withliteral=TTTT
the smallest stretch ofT's
that bbduk will identify will be 4. Depending on what you are doing (kmask=
orktrim=
) sequences will be masked or trimmed.