Unusual FASTQ file

Question

[Nada]

Hi everyone,

I'm master student in bioinformatics field. I need some help plz. I downloaded the fastq file from GEO, but the format I think it's different. I wanna to know what is this..

Why the read is like this ?? I know it should contains (ATGC) not (T2200330123010111..03100022.....023..02.....011022.) here is the format

[Mensur Dlakic]

Bioinformatics Master's Student is not an informative title for your question. I imagine most people will ignore it by assuming that this is someone looking for a student, or a student looking for a position.

The title should tell us something about the problem you are facing rather than something about you. You can still edit it and put something like Unusual FASTQ file or A problem with FASTQ files. Then it will be more likely that those with knowledge of or interest in FASTQ files will read it.

[Ram]

People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more to "job post" than "post on forum" and b) websites there have the ridiculous habit of asking people for unnecessary details (such as job title, date of birth, institute) and making those fields mandatory. People there get used to handing out more information than necessary. To them, the term "Subject" is closer to what we're looking for and would be less ambiguous but we'd introduce similar confusion elsewhere.

Answer 1

[Philipp Bayer]

You have colorspace reads! Here's an old tutorial on converting those: Transforming And Manipulating Color Space Reads There's a script mentioned in this tutorial which does this transformation for you.

I haven't seen those reads in years so I wonder whether they'll be useful for your analysis; it might be really old data. Can you even still buy Solid sequencers?!?

[GenoMax]

This dataset is from 2017 so it is not that old. It is indeed from a 5500W SOLiD sequencer and is in color space.