overlapping regions in bedgraph file prevent creation of bigwig file

[rosbashlab]

chr2L 6026 6046 1
chr2L 6040 6067 1
chr2L 6883 6902 1
chr2L 6987 7008 2
chr2L 8328 8346 1
chr2L 8346 8349 2
chr2L 8349 8378 1

Overlapping regions in bedgraph file is creating errors when I try to create bigwig files from the bedgraph files. I used "bedGraphToBigWig" for this purpose.

In addition, when I used the CITS.pl script I received a bed file out of bound error. There were some entries in the *.tag.uniq.bed file which started from -1. The code worked fine when I removed the out of bound entries from the *.tag.uniq.bed file.

[zhangchaolin]

Hi,
I am surprised that you get overlapping regions if you uses tools in CTK to generate bedGraph files. We will be happy to figure it out what it happens if you can provide the input files and the command line.

For the second question, it could occur in some rare circumstances when the tag is mapped to the extremity of the chromosome, and we still try to get the upstream nucleotide as potential crosslink sites. This is more likely to occur when you included unassembled genomic contig sequences as part of your reference during mapping. A work around for now is to remove those reads, but we will fix this issue for the next release.

Also, we are trying to keep tracking all the questions and answers to better help the research community, so you are welcome to use our CTK user group if you have more questions:

https://groups.google.com/forum/#!members/ctk-user-group

Chaolin

[rosbashlab]

Here is the command line code:
perl tag2profile.pl -v -big -ss -exact -of bedgraph -n "Unique Tag Profile" Hrp48_fusion.tag.uniq.rgb.bed Hrp48_fusion.tag.uniq.bedgraph

Please sort the output bedgraph file to see the overlapping entries.

Hrp48_fusion.tag.uniq.rgb.bed.gz

[zhangchaolin]

could you repost these questions on our CTK user group? We will answer there - a centralized portal is easier us to maintain. Thanks, Chaolin

…

On Sep 19, 2018, at 7:42 PM, rosbashlab ***@***.***> wrote: Here is the command line code: perl tag2profile.pl -v -big -ss -exact -of bedgraph -n "Unique Tag Profile" Hrp48_fusion.tag.uniq.rgb.bed Hrp48_fusion.tag.uniq.bedgraph Please sort the output bedgraph file to see the overlapping entries. Hrp48_fusion.tag.uniq.rgb.bed.gz <https://github.com/chaolinzhanglab/ctk/files/2399047/Hrp48_fusion.tag.uniq.rgb.bed.gz> — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ARL3fXPmdwvuwh2zv13v5drrhxDcQaeRks5uctZpgaJpZM4Wuk9d>.

[rosbashlab]

No problem, I posted it on GitHub. But, I understand that you prefer the Google group. I will post it on the Google group as well.

…

On Wed, Sep 19, 2018, 20:36 zhangchaolin ***@***.***> wrote: could you repost these questions on our CTK user group? We will answer there - a centralized portal is easier us to maintain. Thanks, Chaolin > On Sep 19, 2018, at 7:42 PM, rosbashlab ***@***.***> wrote: > > Here is the command line code: > perl tag2profile.pl -v -big -ss -exact -of bedgraph -n "Unique Tag Profile" Hrp48_fusion.tag.uniq.rgb.bed Hrp48_fusion.tag.uniq.bedgraph > > Please sort the output bedgraph file to see the overlapping entries. > > Hrp48_fusion.tag.uniq.rgb.bed.gz < https://github.com/chaolinzhanglab/ctk/files/2399047/Hrp48_fusion.tag.uniq.rgb.bed.gz > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub < #2 (comment)>, or mute the thread < https://github.com/notifications/unsubscribe-auth/ARL3fXPmdwvuwh2zv13v5drrhxDcQaeRks5uctZpgaJpZM4Wuk9d >. > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AP1bYfk3UdzmyiD-3FkkfsXb34RU_BS9ks5ucuMcgaJpZM4Wuk9d> .

[chaolinzhanglab]

We don’t regularly answer questions posted on GitHub. The google group is the official user group. Chaolin

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On Sep 19, 2018, at 9:11 PM, rosbashlab ***@***.***> wrote: No problem, I posted it on GitHub. But, I understand that you prefer the Google group. I will post it on the Google group as well. On Wed, Sep 19, 2018, 20:36 zhangchaolin ***@***.***> wrote: > could you repost these questions on our CTK user group? We will answer > there - a centralized portal is easier us to maintain. > > Thanks, > Chaolin > > > On Sep 19, 2018, at 7:42 PM, rosbashlab ***@***.***> > wrote: > > > > Here is the command line code: > > perl tag2profile.pl -v -big -ss -exact -of bedgraph -n "Unique Tag > Profile" Hrp48_fusion.tag.uniq.rgb.bed Hrp48_fusion.tag.uniq.bedgraph > > > > Please sort the output bedgraph file to see the overlapping entries. > > > > Hrp48_fusion.tag.uniq.rgb.bed.gz < > https://github.com/chaolinzhanglab/ctk/files/2399047/Hrp48_fusion.tag.uniq.rgb.bed.gz > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub < > #2 (comment)>, > or mute the thread < > https://github.com/notifications/unsubscribe-auth/ARL3fXPmdwvuwh2zv13v5drrhxDcQaeRks5uctZpgaJpZM4Wuk9d > >. > > > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#2 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AP1bYfk3UdzmyiD-3FkkfsXb34RU_BS9ks5ucuMcgaJpZM4Wuk9d> > . > — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ATJh0yVizfL5c98CRaagEIyfWjzJSN8oks5ucusqgaJpZM4Wuk9d>.

[huangyingzhang]

Hi. Have you solved this overlapping problem when using bedGraphToBigWig.