Question: How to remove poly T in RNA-sequencing data
2
gravatar for seta
5.3 years ago by
seta1.4k
Sweden
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
1

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
1
gravatar for h.mon
5.3 years ago by
h.mon31k
Brazil
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
1
gravatar for chen
5.2 years ago by
chen2.1k
OpenGene
chen2.1k wrote:

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

https://github.com/haploxer/after

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
0
gravatar for michael.ante
5.3 years ago by
michael.ante3.6k
Austria/Vienna
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.

Cheers,

Michael

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
0
gravatar for goubert.clement
4.4 years ago by
France
goubert.clement10 wrote:

Hello,

You can also try UrQt: http://lbbe.univ-lyon1.fr/-UrQt-.html 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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