Generate histogram Via BBmap tool
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Entering edit mode
6 weeks ago
Fizzah • 0

Hello there, I am trying to generate histogram for paired end reads via bbmap tool program. However I am getting this output:

root@cemb-ls1-pgs:/mnt/cemb/S017679/raw# /home/fizzah/bbmap/reformat.sh BU21R1.fastq qchist=qchist.txt
java -ea -Xms300m -cp /home/fizzah/bbmap/current/ jgi.ReformatReads BU21R1.fastq qchist=qchist.txt
Executing jgi.ReformatReads [BU21R1.fastq, qchist=qchist.txt]

Set qcount histogram output to qchist.txt
No output stream specified.  To write to stdout, please specify 'out=stdout.fq' or similar.
Input is being processed as unpaired
Input:                      37926174 reads              5726852274 bases
Output:                     37926174 reads (100.00%)    5726852274 bases (100.00%)

Time:                           50.960 seconds.
Reads Processed:      37926k    744.23k reads/sec
Bases Processed:       5726m    112.38m bases/sec

when I specify stream output, it says:

File qchist.txt exists and overwrite=false

Please guide about its solution

histogram bbmap • 214 views
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Entering edit mode

BBMap does not produce graphical output. What you will get is a text based histogram.

In general for all BBMap programs you have to explicitly add option ow=t to overwrite existing files. Be aware that this option instantly wipes the contents of existing files so if you are not careful you can lose data.

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Ok. So can you name some tool that can give graphical outcome based histogram for paired end reads?

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