Hi All,
This is my first post on SEQanswers and I am hoping some help from senior members . I am analyzing sRNA single end sequencing data and using Trimmomatic for trimming adapters. The problem is that after trimming process all the reads are getting dropped. Here is the summary for one file:
As you see, all the trimmed reads have been dropped. I believe that this because of threshold values used - palindrome clip threshold, leading, trailing and sliding window. Should I be using palindrome clip thershold? I would really appreciate it if you can help me with this problem.
Thanks
BADE
This is my first post on SEQanswers and I am hoping some help from senior members . I am analyzing sRNA single end sequencing data and using Trimmomatic for trimming adapters. The problem is that after trimming process all the reads are getting dropped. Here is the summary for one file:
TrimmomaticSE: Started with arguments: -threads 52 -phred64 -trimlog C2.log.txt C2.fastq.gz C2.Processed ILLUMINACLIP:./Trimmomatic-0.32/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 CROP:24 MINLEN:21
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Reads: 39733090 Surviving: 0 (0.00%) Dropped: 39733090 (100.00%)
TrimmomaticSE: Completed successfully
Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Input Reads: 39733090 Surviving: 0 (0.00%) Dropped: 39733090 (100.00%)
TrimmomaticSE: Completed successfully
Thanks
BADE
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