Question: rna seq data trim by trimmomatic
0
gravatar for zh.khodadadi
23 months ago by
zh.khodadadi10
zh.khodadadi10 wrote:

Hi every body

I am going to trim rna seq single end data(Illumina HiSeq 2000) by trimmomatics According to text:

sets of samples were trimmed and filtered with Trimmomatic to remove adapters with up to 2 mismatches, with a palindrome read alignment accuracy of 40 and a sequence match accuracy of 15. This program trimmed reads further by removing leading low-quality or N bases (below quality 3), removing trailing low-quality or N bases (below quality 3), and scanning each read with a 4-base-wide sliding window. The parameters were set for cutting when the average quality per base drops below 15 and then to drop any reads below 36 bases long*

Do these commands exactly refer to text? or need other commands? java -jar trimmomatic-0.36.jar SE -threads 8 -phred33 'path to fastq files' ILLUMINACLIP:TruSeq3-SE:2:30:10 SLIDINGWINDOW:4:15 MINLEN:36

rna-seq commands trimming • 1.1k views
ADD COMMENTlink written 23 months ago by zh.khodadadi10
1

Are you just looking for confirmation? If so, looks good.

ADD REPLYlink written 23 months ago by genomax55k

thanks No, I wanted to understand that are there other commands matches with this text??

ADD REPLYlink written 23 months ago by zh.khodadadi10

The one you have above matches the text posted.

ADD REPLYlink written 23 months ago by genomax55k

Ok, thanks genomax2 .

ADD REPLYlink written 23 months ago by zh.khodadadi10
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