Question: getReadCountsFromBAM and paired-end reads
0
gravatar for Alexandre Kuhn
2.4 years ago by
Alexandre Kuhn20 wrote:

Hello Guenter,

Thank you for your useful package cn.mops.

I use your function "getReadCountsFromBAM". However I noticed that starting from Bioconductor version 3.4, the "mode" argument disappeared (I noticed it as I used to count reads from paired-end sequencing data and setting mode="paired").

This change seems to be due to the fact that you started to rely on exomeCopy::countBamInGRanges from Bioc version 3.4 onwards.

It seems in the current Bioc release 3.5 for instance (and in 3.4), paired-end reads are counted twice. Would there be a straightforward way of counting them only once (i.e. to get the same behavior as in Bioc version 3.3 with mode="paired")?

Thanks for your advice.

Best regards,
Alexandre Kuhn

cn.mops • 442 views
ADD COMMENTlink modified 2.3 years ago • written 2.4 years ago by Alexandre Kuhn20
Answer: getReadCountsFromBAM and paired-end reads
0
gravatar for Günter Klambauer
2.3 years ago by
Austria
Günter Klambauer540 wrote:

Dear Alexandre,

We have changed the read-counting procedure due to errors that were reported by several users in the last Bioc release. For simplicity, we have used the read-counting function of "exomecn.mops" which worked well empirically. However, for some purposes (such as whole genome sequencing with medium or low coverage) the original function might work better. I currently do not find time to re-implement this function (with paired-end reads only counted once at the middle position), but if you -- or any other user -- would implement it (or update the function of the former cn.mops versions), I would be happy to include it in the package! I am sorry that I cannot give a more positive reply!

Regards,

Günter

ADD COMMENTlink written 2.3 years ago by Günter Klambauer540
Answer: getReadCountsFromBAM and paired-end reads
0
gravatar for Alexandre Kuhn
2.3 years ago by
Alexandre Kuhn20 wrote:

Thanks for your explanations.

Could you please provide a pointer to the errors that were reported with the previous "getReadCountsFromBAM" function?

It would help me to understand if the counting I did using cn.mops in Bioc 3.3 gave accurate results, as well as maybe provide some ideas on how to reimplement/update that function (as per your suggestion).

Alexandre

ADD COMMENTlink written 2.3 years ago by Alexandre Kuhn20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 268 users visited in the last hour