raymondkiu / fastq-info Goto Github PK

Hi Raymond,

Thanks so much for providing this tool. It worked great.

I was wondering if the same could be done for long reads, more specifically Oxford Nanopore?

Thanks :)

Hi @raymondkiu I'm really keen to try your coverage script and was wondering can multiple samples be run at the same time using a loop?

I must be upfront and say I'm new to the world of scripts/command so I'm not that savvy! Normally for writing a loop I do something like this:

1 #!/bin/sh
2
3 sampleLoc=/Path/to/fq.gz/
4 sampleName= ("19IE01" "19IE02" "19IE03" "19IE04" "19IE05" )
5 outputLoc=/Path/to/Output/
6
7 for sample in ${sampleName[*]}
8
9 do
10
11 spades.py -1 $sampleLoc/${sample}R1.fq.gz -2 $sampleLoc/${sample}R2.fq.gz -o
$outputLoc/${sample}
12
13 done

Can I add something similar to the ./fastq_info_3.sh file to loop all the .fq.gz files?

Cheers