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Foward only surviving reads but no reverse only surviving and no dropped reads #56

Open Catv97 opened 9 months ago

Catv97 commented 9 months ago

iI run trimmomatic v0.39 for my paired end reads and I get this output: TrimmomaticPE: Started with arguments: -threads 12 -phred33 SR22799322_1.fastq.gz SRR22799322_2. fastq.gz /home/projects/ossabaw/samples/SR413590_yaolei/trimmed/SRR22799322_TRIM_1P.fastq.gz /home/projects/ossabaw/samples/SR413590_yaolei/trimmed/SRR 22799322_TRIM_1U.fastq.gz /home/projects/ossabaw/samples/SR413590_yaolei/trimmed/SR22799322_TRIM_2P.fastq.gz /home/projects/ossabaw/samples/SR413590_yaolei/trimmed/SRR22799322_TRIM_2U.fastq.gz ILLUMINACLIP:/ho me/projects/ossabaw/samples/SR413590_yaolei/adaptersPE.fa:2:30:10 MINLEN:50 Using PrefixPair: " AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' and AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, o forward only sequences, 0 reverse only sequences Input Read Pairs: 68170396 Both Surviving: 68088438 (99.88%) Forward Only Surviving: 81958 (0.12%) Reverse Only Surviving: 0 (0.00%) Dropped: 0 (0.00%) TrimmomaticE: Completed successfully

And I do not understand why I have forward only surviving reads. My initial files (before running trimmomatic) had the same number of sequences when checked with fastqc.

hoppo commented 8 months ago

Is is just a copy/paste issue that the input files are called:- SR22799322_1.fastq.gz SRR22799322_2. fastq.gz

the first file only had a single R (SR2.. v SRR2..) and there is a space in the second file.

Catv97 commented 8 months ago

yes that is just a copy mistake, sorry about that.