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

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Catv97 opened this issue Oct 25, 2023 · 2 comments

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@Catv97
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Catv97 commented Oct 25, 2023

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
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hoppo commented Nov 8, 2023

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
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Catv97 commented Nov 9, 2023

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

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