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Hii dear friends
I have a question about Trimmomatic. I wrote this command:
java -jar /usr/bin/trimmomatic-0.33.jar PE -phred64 72_L3_1.fq.gz 72_L3_2.fq.gz 71P_1.fq.gz 71UP_1.fq.gz 71P_2.fq.gz 71UP_2.fq.gz ILLUMINACLIP:Over.fasta:2:40:15
72_L3_1.fq.gz
and
72_L3_2.fq.gz
are my input files
71P_1.fq.gz
71UP_1.fq.gz
71P_2.fq.gz
and
71UP_2.fq.gz
are my output files. In my case P means paired and UP means unpaired.
after I did fastqc I got overrepresented sequence (it is not adapter) and I stored it in Over.fasta and I want to trim it from my data.
but when I run the command I see this:
ILLUMINACLIP: Using 0 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 19759652 Both Surviving: 19759652 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
It does not trim the sequence.
Why it is like that?
In addition, for Palindrome and Single mode U just selected 40 and 15 because the manual selected them. Actually I do not know which score I should select. How can I choose the correct score?
Would you please help me in these two questions.
-------------------------------------------------------------------
I'm sorry for asking so many questions each day. I' working with RNA-seq data in these days. In each level, I should stop due to errors, warnings, blocks and confusions and this story continues.
and thank you for helping me in solving all these problems.
I have a question about Trimmomatic. I wrote this command:
java -jar /usr/bin/trimmomatic-0.33.jar PE -phred64 72_L3_1.fq.gz 72_L3_2.fq.gz 71P_1.fq.gz 71UP_1.fq.gz 71P_2.fq.gz 71UP_2.fq.gz ILLUMINACLIP:Over.fasta:2:40:15
72_L3_1.fq.gz
and
72_L3_2.fq.gz
are my input files
71P_1.fq.gz
71UP_1.fq.gz
71P_2.fq.gz
and
71UP_2.fq.gz
are my output files. In my case P means paired and UP means unpaired.
after I did fastqc I got overrepresented sequence (it is not adapter) and I stored it in Over.fasta and I want to trim it from my data.
but when I run the command I see this:
ILLUMINACLIP: Using 0 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 19759652 Both Surviving: 19759652 (100.00%) Forward Only Surviving: 0 (0.00%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%)
It does not trim the sequence.
Why it is like that?
In addition, for Palindrome and Single mode U just selected 40 and 15 because the manual selected them. Actually I do not know which score I should select. How can I choose the correct score?
Would you please help me in these two questions.
-------------------------------------------------------------------
I'm sorry for asking so many questions each day. I' working with RNA-seq data in these days. In each level, I should stop due to errors, warnings, blocks and confusions and this story continues.
and thank you for helping me in solving all these problems.
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