# Query regarding HMP2 Metatranscriptomics raw files **URL:** \ **Category:** IBDMDB\ **Created:** [January 27, 2021, 1:07pm UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616 "2021-01-27T13:07:08Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![PRATIK\_SHINDE](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/pratik_shinde/32/287_2.png) [@PRATIK\_SHINDE](https://forum.biobakery.org/u/PRATIK_SHINDE)\ **Post date:** [January 27, 2021, 1:07pm UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616/1 "2021-01-27T13:07:08Z")
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 ---
**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Post date:** [January 29, 2021, 4:09pm UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616/2 "2021-01-29T16:09:36Z")
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 ---
**Author:** ![PRATIK\_SHINDE](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/pratik_shinde/32/287_2.png) [@PRATIK\_SHINDE](https://forum.biobakery.org/u/PRATIK_SHINDE)\ **Post date:** [February 5, 2021, 2:42pm UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616/3 "2021-02-05T14:42:40Z")
Hello Sir, Thank you for reply, I can tell you one of the sample ID of metatranscriptomics sample, such as CSM7KOUN ---
**Author:** ![Ish](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ish/32/195_2.png) [@Ish](https://forum.biobakery.org/u/Ish)\ **Post date:** [April 1, 2021, 9:01pm UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616/4 "2021-04-01T21:01:48Z")
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 ---
**Author:** ![PRATIK\_SHINDE](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/pratik_shinde/32/287_2.png) [@PRATIK\_SHINDE](https://forum.biobakery.org/u/PRATIK_SHINDE)\ **Post date:** [April 2, 2021, 6:54am UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616/5 "2021-04-02T06:54:44Z")
Hello @Ish The preprocessing steps used on the raw reads are mentioned on Biobakery GitHub website [biobakery\_workflows · biobakery/biobakery Wiki · GitHub](https://github.com/biobakery/biobakery/wiki/biobakery_workflows) 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 ---
**Author:** ![Ish](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ish/32/195_2.png) [@Ish](https://forum.biobakery.org/u/Ish)\ **Post date:** [April 5, 2021, 1:39pm UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616/6 "2021-04-05T13:39:56Z")
Thanks @PRATIK_SHINDE Just making sure- the preprocessing is detailed under \* [**2.3.1 Quality control data**] (and actually in [kneadata](http://huttenhower.sph.harvard.edu/kneaddata)? ([biobakery\_workflows · biobakery/biobakery Wiki · GitHub](https://github.com/biobakery/biobakery/wiki/biobakery_workflows#231-quality-control-data)) ---
**Author:** ![PRATIK\_SHINDE](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/pratik_shinde/32/287_2.png) [@PRATIK\_SHINDE](https://forum.biobakery.org/u/PRATIK_SHINDE)\ **Post date:** [April 5, 2021, 2:01pm UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616/7 "2021-04-05T14:01:44Z")
Hello @Ish , You can check the respective sample files log file, available at ibdmdb for detailed preprocessing and for commands detail check kneadata manual ---
**Author:** ![PRATIK\_SHINDE](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/pratik_shinde/32/287_2.png) [@PRATIK\_SHINDE](https://forum.biobakery.org/u/PRATIK_SHINDE)\ **Post date:** [May 4, 2021, 12:47pm UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616/8 "2021-05-04T12:47:46Z")
Hi @sagunmaharjann , Will you please reply to my query, it has been 3 months since we started the conversation. thank you ---
**Author:** ![sagunmaharjann](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/sagunmaharjann/32/168_2.png) [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Post date:** [May 4, 2021, 5:29pm UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616/9 "2021-05-04T17:29:20Z")
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 ---
**Author:** ![PRATIK\_SHINDE](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/pratik_shinde/32/287_2.png) [@PRATIK\_SHINDE](https://forum.biobakery.org/u/PRATIK_SHINDE)\ **Post date:** [May 4, 2021, 5:57pm UTC](https://forum.biobakery.org/t/query-regarding-hmp2-metatranscriptomics-raw-files/1616/10 "2021-05-04T17:57:48Z")
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.