Hi All.
I'm using a ramdom amplification protocol and for library preparation I'm using Nextera XT. I'm performing seq step with Miseq reagent kit v3 600 cycles but i only use 200 cycles instead of 300 in order to get better quality score.
After adapters trimmed with Trimmomatic I've got this result:
TrimmomaticPE: Started with arguments:
-phred33 -trimlog 12143_trimlog.txt 12143_R1.fastq.gz 12143_R2.fastq.gz 12143_FWP.fq.gz 12143_FWUP.fq.gz 12143_REVP.fq.gz 12143_REVUP.fq.gz ILLUMINACLIP:/home/dell/miniconda3/share/trimmomatic/adapters/NexteraPE-PE.fa:2:30:10
Multiple cores found: Using 4 threads
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 2764988 Both Surviving: 658763 (23.83%) Forward Only Surviving: 2105922 (76.16%) Reverse Only Surviving: 288 (0.01%) Dropped: 15 (0.00%)
TrimmomaticPE: Completed successfully
FastQC basic statistics for forward before triimmig
Encoding Sanger / Illumina 1.9
Total Sequences 2764988
Sequences flagged as poor quality 0
Sequence length 201
%GC 42
FastQC basic statistics for forward paired after triimmig
Encoding Sanger / Illumina 1.9
Total Sequences 658763
Sequences flagged as poor quality 0
Sequence length 1-201
%GC 41
Why I have a very low % of both surviving and why a high value for forward only?
I really appreciate your feedbacks.
thanks
Chris
I'm using a ramdom amplification protocol and for library preparation I'm using Nextera XT. I'm performing seq step with Miseq reagent kit v3 600 cycles but i only use 200 cycles instead of 300 in order to get better quality score.
After adapters trimmed with Trimmomatic I've got this result:
TrimmomaticPE: Started with arguments:
-phred33 -trimlog 12143_trimlog.txt 12143_R1.fastq.gz 12143_R2.fastq.gz 12143_FWP.fq.gz 12143_FWUP.fq.gz 12143_REVP.fq.gz 12143_REVUP.fq.gz ILLUMINACLIP:/home/dell/miniconda3/share/trimmomatic/adapters/NexteraPE-PE.fa:2:30:10
Multiple cores found: Using 4 threads
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Read Pairs: 2764988 Both Surviving: 658763 (23.83%) Forward Only Surviving: 2105922 (76.16%) Reverse Only Surviving: 288 (0.01%) Dropped: 15 (0.00%)
TrimmomaticPE: Completed successfully
FastQC basic statistics for forward before triimmig
Encoding Sanger / Illumina 1.9
Total Sequences 2764988
Sequences flagged as poor quality 0
Sequence length 201
%GC 42
FastQC basic statistics for forward paired after triimmig
Encoding Sanger / Illumina 1.9
Total Sequences 658763
Sequences flagged as poor quality 0
Sequence length 1-201
%GC 41
Why I have a very low % of both surviving and why a high value for forward only?
I really appreciate your feedbacks.
thanks
Chris
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