Question

Kmer sequences in 5' RNAseq reads

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9.3 years ago

silas008 ▴ 170

Should I to trim the first bases of RNAseq reads that contain 7_k-mer?

K-mer RNA-Seq • 2.0k views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by silas008 ▴ 170

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First why do you want to trim first 7_k-mers ? Do u think they have very poor quality or they are adapter contaminations ? What your pipeline ? Expression or Assembly or something else ?

ADD REPLY • link 9.3 years ago by GouthamAtla 12k

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I don't know how to put images here to exemplify my question. :(

ADD REPLY • link 9.3 years ago by silas008 ▴ 170

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upload them to some image hosting site and post the link here.

ADD REPLY • link 9.3 years ago by h.mon 35k

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try uploading to google+, and paste the link here.

ADD REPLY • link 9.3 years ago by venu 7.1k

score 1 · Answer 1 · 2015-08-09

No, at least, not blindly. Even though FastQC will tell you the "per base sequence content" is problematic, and in general one can easily spot the first 5-10 bases as being non-randomly distributed, this does not necessarily means they are wrong. If you are really worried, you could map (or assemble and map, if you do not have a reference at hand) and check the alignment, if these bases do not align correctly, then you can trim.