Entering edit mode
6.8 years ago
luyang1005
▴
20
Hi,
May I know is that possible to trim the reads to the same region? Here is the situation. One batch of sequence reads are sequenced by 515F-806R, the other one is sequenced by 341F-806R. May I know how to compare the results? Thanks in advance.
It's entirely unclear what you aim to do with the results.
OP is likely referring to 16S amplicons.
Guess you are looking to trim 341F-806R dataset so it becomes similar to 515F-806R. You should be able to do that with
bbduk.shfrom BBMap. Something likebbduk.sh in=orig.fa out=trim.fa ftl=174Hmm, I need to work on my crystal-ball skills it seems. And I got confused by the
rna-seqtag.Both us could be wrong until OP confirms one way or other. I stopped looking at tags a while ago.
Hi, thanks so much for your suggestion. Sorry for the unclear description. You guess is completely right. It seems that BBDUCK will force to trim the head 174bp reads. Does that mean I can get the relatively reasonable result? Does my thinking make sense?
You should end up with the same region (assuming your sequencing has worked as expected) as the shorter set of results. I suggest inspecting the resulting reads to make sure things look ok after you trim them using
bbduk.sh.Hi, I have two batches of 16S Illumina sequencing files, which were sequenced by two primers, one is 515F-806R, while the other is 341F-806R. I want to compare the two batches together. Honest to say I am not familiar with the sequencing data processing. Therefore I want to trim the 341F-806R to the same region or length, then compare them. Is there any other way to deal with this? Thanks in advance.
I had noted one way of doing this above. If your results are in fastq format then use this command line
bbduk.sh in=orig.fq.gz out=trim.fq.gz ftl=174(BBmap Suite).Your suggestion works on the trimming well. But result shows me that trimming is not perfect. I will try another way around.
Anyway, I learned a new method. Thanks for your kindness.
The command list I had posted does a hard-trimming of length 174 bp from left end of read.
Perhaps I should have asked first as to how long your reads are (if they were merged from PE data and trimmed to remove adapters then they may indeed be 806-341 = ~465 bp). If they are not merged/long then a hard-trim like that is going to cause problems. We will need a different strategy in that case.