... paired-end reads into two FASTq files using the "outReadsUnmapped - Fastx" option, then the resulting files are out-of-order, i.e. mates of the ...
In certain cases, you need to sort FASTQ files by their sequence identifiers (e.g. to fix the order of paired-end or mate-pair sequences). There are several
Istvan is right. You will spend more time in figuring out how to put reads in proper order than reprocessing the original fastq files from scratch using trimmomatic. It ...
A lot of software benefits from paired fastq files that contain mate pair
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Presumably the mispaired read corresponds to the first read in the out-of-order file.
and writes several output files, such as alignments (SAM/BAM), mapping
1, the member of a pair, 1 or 2 (paired-end or mate-pair reads only). Y, Y if the
Paired end reads are usually provided as two fastq-format files, with each file
mcdonaldlab.biology.gatech.edu
out_tag, A string for the output SAM file suffix. Resulting file will
is two FASTQ files containing read 1 and read 2 of each mate pair, respectively, in the same