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rreformat.sh and stats.sh program in BBmap

Hello there, i am working with RNA seq data and have paired end reads. While running the reformat.sh command I am getting this out put:

Set INTERLEAVED to false Exception in thread "main" java.lang.AssertionError: File 19213R-08-01_S16_L002_R1_001.fastq exists and overwrite=false

what does it mean?

Also while working with paired end reads and calculating their read information with stats.sh program, is there any way to get the out put of both R1 and R2 files simultaneously in one file?

stats.sh reformat.sh
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written by Fizzah • Fizzah

1 answer

Looks like you are trying to overwrite a file that already exists. If you don't want to do that then provide a different name to write the output to. If you do want to overwrite it (remember the file will be replaced with new content) then add option ow=t.

Stats for read numbers are calculated for individual files, getting output of two files simultaneously will not make sense.

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written by GenoMax GenoMax

while working with paired end reads, both R1 and R2 files per sample gives same output. so while compiling data what will be the best way to describe it?

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written by Fizzah • Fizzah

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