Question

Getting just fastqc.zip file?

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6.7 years ago

star ▴ 350

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

RNA-Seq fastqc • 5.3k views

ADD COMMENT • link updated 5.4 years ago by vinay.rs ▴ 10 • written 6.7 years ago by star ▴ 350

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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 REPLY • link 6.7 years ago by GenoMax 147k

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

ADD REPLY • link 6.7 years ago by Bastien Hervé 5.9k

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unable to open the zip

ADD REPLY • link 5.4 years ago by abhilashdasari.10 ▴ 30

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use unzip tool to unzip the zip file.

ADD REPLY • link 5.4 years ago by vinay.rs ▴ 10

score 1 · Answer 1 · 2018-03-05

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6.7 years ago

vinay.rs ▴ 10

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

ADD COMMENT • link 6.7 years ago by vinay.rs ▴ 10