Question: Getting just fastqc.zip file?
0
gravatar for star
12 months ago by
star130
Netherlands
star130 wrote:

I am new user in RNA-seq data, I am trying to do fastqc analysis with Linux, but when I run fastqc command on my data it gives me only fastqc.zip file and not .html file or anything else to see plots.

fastqc -t 8 -o Raw-data/RNA-seq/qc/ Documents/S22_L001_R1_001.fastq
fastqc rna-seq • 673 views
ADD COMMENTlink modified 12 months ago by vinay.rs0 • written 12 months ago by star130
2

See if this is applicable: FastQC not making html output report.

Also make sure you are running fastqc in non-interactive mode. If you are using interactive-mode/GUI then follow these directions to save a report in html.

ADD REPLYlink modified 12 months ago • written 12 months ago by genomax64k
1

Please, insert your command line to your post, to find out what's going on

ADD REPLYlink modified 12 months ago • written 12 months ago by Bastien Hervé3.7k
0
gravatar for vinay.rs
12 months ago by
vinay.rs0
IISc
vinay.rs0 wrote:

Unzip the zip file, you will have html file called fastqc_report.html inside.

ADD COMMENTlink modified 12 months ago • written 12 months ago by vinay.rs0
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