Hello,
This thread helped me with an issue I'm dealing with only I've become stuck and seek some advice.
I am trying to use BBMap or BBTools to fix what might be either an incorrectly interleaved file or a file that has reads formatted as single-end but really contains a collection of paired and single end reads.
I have interleaved some paired-end RNAseq Illumina reads in order to run them through a program called 'sortmerna' to remove rRNA from my reads. Here is a testformat.sh on the interleaved input file.
If BBTools can provide this ability (filter out rRNA), I would appreciate any advice. The output file seems to either be incorrectly interleaved or are just in single end format. Here is a testformat.sh of the output file I am interested in.
I would ultimately like to the reads from this output file and separate them by their forward and reverse reads into two files; essentially I want to map them with tophat.
Is anyone familiar with BBTools and how to fix such an issue? I've hit a roadblock.
This thread helped me with an issue I'm dealing with only I've become stuck and seek some advice.
I am trying to use BBMap or BBTools to fix what might be either an incorrectly interleaved file or a file that has reads formatted as single-end but really contains a collection of paired and single end reads.
I have interleaved some paired-end RNAseq Illumina reads in order to run them through a program called 'sortmerna' to remove rRNA from my reads. Here is a testformat.sh on the interleaved input file.
Code:
/mnt/home/steepale/Apps/bbmap/testformat.sh ./data/017798-1_1_AGTGAG_L001_interleaved_001_100K.fastq sanger fastq raw interleaved 125bp
If BBTools can provide this ability (filter out rRNA), I would appreciate any advice. The output file seems to either be incorrectly interleaved or are just in single end format. Here is a testformat.sh of the output file I am interested in.
Code:
/mnt/home/steepale/Apps/bbmap/testformat.sh ./data/017798-1_1_AGTGAG_L001_norRNA_001_100K.fastq -1 fastq raw single-ended
I would ultimately like to the reads from this output file and separate them by their forward and reverse reads into two files; essentially I want to map them with tophat.
Is anyone familiar with BBTools and how to fix such an issue? I've hit a roadblock.
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