Question: How to remove poly T in RNA-sequencing data
gravatar for seta
5.3 years ago by
seta1.4k wrote:

Hi all,

I'm using Trim_galore tool for quality and adaptor trimming, but I found no option to remove poly T in the sequencing data resulted from poly A enrichment libraries sequencing. Could anybody please let me know how should remove poly T in data? Thanks

ADD COMMENTlink modified 4.4 years ago by goubert.clement10 • written 5.3 years ago by seta1.4k

Have you tried mapping the RNA-seq data yet? It may not be necessary to remove polyA stretches because they won't map to a unique location and you may already have enough reads to not worry about it. Another poster asked a similar question Statistics About Poly-A Tails In Rnaseq Reads .

However there are other posts that may help you such as:

Trim Poly-A Tail And Trailing Nucleotides


ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by Jason900
gravatar for h.mon
5.3 years ago by
h.mon31k wrote:

It is not clear-cut trimming poly-A tails is beneficial, are you certain you need to trim the poly-A tail? As Jason pointed, many short read mappers won't be affected by poly-A tails. For assembly, it may help discern splice variants (see comment on MIRA's manual).

ADD COMMENTlink written 5.3 years ago by h.mon31k
gravatar for chen
5.2 years ago by
chen2.1k wrote:

There is a tool available on Github for removing PolyA, PolyT, PolyC, PolyG

Automatic Filtering, Trimming, and Error Removing for fastq data
Currently it supports Illumina 1.8 or newer format
AFTER can simply go through all fastq files in a folder and then output a good folder and a bad folder, which contains good reads and bad reads of each fastq file

Besides remove PolyX, it also can do:
Trim reads at front and tail according to bad per base sequence content
Detect and eliminate bubble artifact caused by sequencer due to fluid dynamics issue
Filter low-quality reads

ADD COMMENTlink written 5.2 years ago by chen2.1k
gravatar for michael.ante
5.3 years ago by
michael.ante3.6k wrote:

You can use bbduk from the bbmap suite. Just create a polyA.fa (e.g. ">polyA\nAAAAAAAAAAAAA")  and zip it into the bbmap resources folder; run then bbduk with ref=resources/polyA.fa.gz . Maybe it is necessary to add a polyT sequence into your fasta.
I'm quite sure you can add the sequences to the adapter-file of trim_galore likewise.



ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by michael.ante3.6k

Thanks for all help.

ADD REPLYlink written 5.3 years ago by seta1.4k
gravatar for goubert.clement
4.4 years ago by
goubert.clement10 wrote:


You can also try UrQt: It performs poly-N trimming as well as quality trimming, searching for the best larger fragment in the whole read. It has a high percentage of base conservation. It is pretty effective.

ADD COMMENTlink written 4.4 years ago by goubert.clement10
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