Read count doesn't update about fastq.bio HOT 7 CLOSED

Glad you like it!

I have a few questions to help diagnose this issue:

• Can you send me the FASTQ file you used (or just the top 2K reads)?
• Do you see the same "0K" issue when you click on "Use Sample FASTQ"?

from fastq.bio.

Hi @robertaboukhalil I don't have the same issue with the sample fastq (good question!).

It also works with the Platinum Genomes fastqs.

I am not be able to send you a fastq as I'm working on clincal data. But if I zcat the first 4000 reads and dump them in a new fastq, then gzip it works. I shall try to dig out a research run and see whether we get the same issue.

PS I'm using Chrome Version 61.0.3163.79 (Official Build) (64-bit)

from fastq.bio.

That's strange, can you check the console log as well? It should tell you how many reads are being read.

from fastq.bio.

This is the console log I get. The first set of output is for my "normal" fastq file (up to the first line marked 5️⃣ ). The second set is the "test" fastq file, which is just the first 3000 reads from the "normal" one. Very strange.

from fastq.bio.

That is strange indeed. Just to make sure, the first set of output is your gzipped FASTQ, and the second set of output where you did zcat -> gzip on it?

If so, it may be that the first file was gzipped in a different way that isn't supported here?

Can you try running the file command on your original file: file original_fastq.gz and see if it says something other than gzip compression?

from fastq.bio.

Ah there is a difference between the pipeline derived fastq.gz and the subsequent downsampled version I created. I wonder what it is!?

$ file pipeline_output.fastq.gz
pipeline_output.fastq.gz: gzip compressed data, extra field

$file test.fastq.gz 
test.fastq.gz: gzip compressed data, was "test.fastq", last modified: Tue Sep 12 14:48:24 2017, from Unix

from fastq.bio.

Interesting, I don't usually see the "extra field" part when running file. It's possible the library I'm using for gzip parsing doesn't support those extra fields.

from fastq.bio.