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Question: Regarding splitter or merging the paired end sequencing file
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gravatar for DL
17 months ago by
DL • 0
DL • 0 wrote:

hello, Recently i got paired end data and firstly, i removed the adopter sequences. For that i used fastx_clipper but i got the number of reads are different in R1 and R2. So i searched the solution for that on biostars and i found that ppl first merging the R1 and R2 files then do filtering for removal of low quality reads and then use splitter program for split the files.

So any one can tell me that is it correct method and one more thing i want to ask that after merging the R1 and R2 files, can i remove the adopter from merged file using Fastx_clipper then i can split the files in R1 and R2.

Please tell me which steps will be good.

Thanks
rna-seq galaxy assembly • 878 views
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modified 17 months ago by y.hoogstrate • 460 • written 17 months ago by DL • 0
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gravatar for y.hoogstrate
17 months ago by
y.hoogstrate • 460
Netherlands
y.hoogstrate • 460 wrote:

This can be a frustrating problem as the order in the file is often used to link R1 and R2 files rather than the names of the sequencing reads. The tools Sickle (low quality trimming only) and Trimmomatic are aware of this and put the reads of which the mate has been discarded in a separate file. This preserves the order of the mates of which both mates are preserved.

I don't get what you mean with merging R1 and R2 files. Aligners (STAR, HISAT) have the option to align paired-end sequencing data with a separate file for R1 and a separate file for R2. This is to my knowledge the standard way of working with paired-end RNA-seq data.
ADD COMMENT • link modified 17 months ago • written 17 months ago by y.hoogstrate • 460
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