build my own gc and map rds file

[jinghu23]

Hi, I just tried to use fragCounter to obtain corrected read depth data and I got some error infos. It looks like some goes wrong with the gc file. I guess the GC file you offer is for WGS, however my bam files are from panel sequencing. So I wonder how to make the GC and mappability files? Thanks in advance~

Jay

[mskilab]

You will need to harmonize the gc and mappability files with your read depth data so the bins are the same One easy way is as follows: (using the gUtils operation %$%, assuming everything is a GRanges - it aggregates ie averages the data on the right hand side with the ranges on the left) gcpanel = rdpanel[, c()] %$% gcwgs mappanel = rdpanel[, c()] %$% mapwgs

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On Wed, Oct 7, 2020 at 10:31 PM jinghu23 ***@***.***> wrote: Hi, I just tried to use fragCounter to obtain corrected read depth data and I got some error infos. It looks like some goes wrong with the gc file. I guess the GC file you offer is for WGS, however my bam files are from panel sequencing. So I wonder how to make the GC and mappability files? Thanks in advance~ Jay — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AC73JEN5DGW5Q376UNWDQ2TSJUP7LANCNFSM4SIE7FJQ> .

[jinghu23]

You will need to harmonize the gc and mappability files with your read depth data so the bins are the same One easy way is as follows: (using the gUtils operation %$%, assuming everything is a GRanges - it aggregates ie averages the data on the right hand side with the ranges on the left) gcpanel = rdpanel[, c()] %$% gcwgs mappanel = rdpanel[, c()] %$% mapwgs
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On Wed, Oct 7, 2020 at 10:31 PM jinghu23 @.***> wrote: Hi, I just tried to use fragCounter to obtain corrected read depth data and I got some error infos. It looks like some goes wrong with the gc file. I guess the GC file you offer is for WGS, however my bam files are from panel sequencing. So I wonder how to make the GC and mappability files? Thanks in advance~ Jay — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC73JEN5DGW5Q376UNWDQ2TSJUP7LANCNFSM4SIE7FJQ .

Thx for ur reply. However, I was confused by what u list above. Does rdpanel mean the read depth info of panel? So should I process the panel rd data before feed to fragCounter to construct the PON?

[xtYao]

You will need to harmonize the gc and mappability files with your read depth data so the bins are the same One easy way is as follows: (using the gUtils operation %$%, assuming everything is a GRanges - it aggregates ie averages the data on the right hand side with the ranges on the left) gcpanel = rdpanel[, c()] %$% gcwgs mappanel = rdpanel[, c()] %$% mapwgs
…
On Wed, Oct 7, 2020 at 10:31 PM jinghu23 @.***> wrote: Hi, I just tried to use fragCounter to obtain corrected read depth data and I got some error infos. It looks like some goes wrong with the gc file. I guess the GC file you offer is for WGS, however my bam files are from panel sequencing. So I wonder how to make the GC and mappability files? Thanks in advance~ Jay — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#6>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AC73JEN5DGW5Q376UNWDQ2TSJUP7LANCNFSM4SIE7FJQ .

Thx for ur reply. However, I was confused by what u list above. Does rdpanel mean the read depth info of panel? So should I process the panel rd data before feed to fragCounter to construct the PON?

I believe rdpanel represents the GRanges of the genomic bins covering the effective targets of the capturing panel you are using. For example, if a panel only covers GRanges("1:1-400"), then rdpanel is GRanges(c("1:1-200", "1:201-400")). Just like in WGS we divide the whole genome into bins, here you are just dividing the subset of genomic regions covered by the panel.