The bioBakery help forum

Query regarding HMP2 Metatranscriptomics raw files

Data resource IBDMDB
#1

Hello Sir,
I am doing reanalysis of your metatranscriptomics data. In raw metatranscriptomics files which were passed through quality control pipeline using #infrastructure-and-utilities:kneaddata Kneaddata, The output is concatenated and I want to seperate forward read (#0/1)and reverse read(#0/2). I could not understand how to identify some reads as they only had #0 at the end of the read ID.

Also please tell me if my consideration of forward read and reverse read ID is correct or not
Thank you

#2

Hi Pratik,

Yes, you are right about the forward read and reverse read ID. Can you point me out (link) to the raw metatranscriptomics files which have #0 at the end?

Thanks

#3

Hello Sir,
Thank you for reply, I can tell you one of the sample ID of metatranscriptomics sample, such as CSM7KOUN

#4

Hi @PRATIK_SHINDE and @sagunmaharjann,
I also downloaded these data from idbmdb. I understand the fastq files are interleaved paired end. Did you managed to understand what are the #0 reads?
Additionally, I’m wondering which preprocessing steps the reads were subjected to.
Thanks

#5

Hello @Ish
The preprocessing steps used on the raw reads are mentioned on Biobakery GitHub website biobakery_workflows · biobakery/biobakery Wiki · GitHub

It’s mentioned in detail here.
As for the #0 reads I am still not sure what they are and waiting for reply from @sagunmaharjann

#6

Thanks @PRATIK_SHINDE
Just making sure- the preprocessing is detailed under * [ 2.3.1 Quality control data ] (and actually in kneadata? (biobakery_workflows · biobakery/biobakery Wiki · GitHub)

#7

Hello @Ish ,
You can check the respective sample files log file, available at ibdmdb for detailed preprocessing and for commands detail check kneadata manual

1 Like
#8

Hi @sagunmaharjann ,
Will you please reply to my query, it has been 3 months since we started the conversation.
thank you

#9

Hi @PRATIK_SHINDE ,

Apologies for the delay. I compared and tested a couple of MTX samples that you pointed out and the #0 are the forward reads “#0/1”. The old version of Kneaddata was somehow removing the “/1” from the forward reads during the merge.

Regards,
Sagun

#10

Hi @sagunmaharjann,
Thanks for reply, so does that mean almost 80% of the reads are forward reads only. That’s the same issue with other sample files.