-
Notifications
You must be signed in to change notification settings - Fork 113
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
[Feature request] Add tag for reporting number of converted/unconverted bases #328
Comments
Hello Chang, Thank you very much for this issue!!! I introduced this bug in last commit ( There are 4 different cases a read can be mapped to reference(genome): Yf tag will report the conversion number. For example, with XM tag will report mismatch and not include Yf tag. For example with
Yf is 3. XM is 2. The MD tag will show all the differences between reference and read sequence. So the MD tag should be: Sorry again for the bug. |
By reading the code, I found that |
Thank you very much @imzhangyun. Can I have another tag, like |
Thank you for your suggestion. Since the Also
In this case, Best, |
How about make all the tags optional, just in the same way as STAR aligner do? I wonder if there is any concern to make Yn + Yf= C counts? |
Hello Chang, Sorry for the last response. I just add a new tag
In this case, Too get the Best, |
Cool. Thank you very much for your help.
…On Fri, Oct 8, 2021 at 2:58 PM Yun (Leo) Zhang ***@***.***> wrote:
Hello Chang,
Sorry for the last response. I just add a new tag Zf:i:<N>. The Zf tag
counts the unconverted base in the read sequence.
Reference Sequence: NNNNNNNAAACCCCCCGGGGGTTTTTTTTTNNNNNNNNN
** --- ****
Read Sequence: AAAGGCTTTGGGGGTTTTTCCCC
In this case, Zf = 1, Yf = 3, XM = 6. (--base-change C,T)
Too get the HISAT-3N with Zf tag, please check our "hisat-3n_Zf" branch.
I tested it and it looks OK. Could you also test it and see if it works for
you? Then I will merge it to the "hisat-3n' branch.
Best,
Leo
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
<#328 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABJKEVWXYCFXOIKM2SL4PCLUF5ENFANCNFSM5FSCE6ZQ>
.
Triage notifications on the go with GitHub Mobile for iOS
<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
or Android
<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
|
The
Yf
tag in hisat2-3n is a little confusing. When run hisat2-3n with--base-change C,T
argument, I guess the "number of conversion" should be the number of C bases that converted into T. But I found that this tag is reporting other kinds of mutations (mismatch), say G to T mutation, and the number of C to T mutation is not included. However, theXM
tag reports the exact number of C to T conversion. This looks very weird, because theYf
andXM
tag are documented asI would like to know if it is possible to report number of non C to T conversion in to XM tag, and use another two tags to report number of C to T conversion and number of non C to T conversion?
C to T is an example, this can also be applied to other settings.
The text was updated successfully, but these errors were encountered: