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HiCUP
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How to prepare HiCUP BAM output as input for HOMER?
HOMER
HiCUP
BAM
HiC
2.6 years ago
Ankit
▴ 20
0
votes
9
replies
1.5k
views
from denove contig assembly to chromosome bins
diffhic
gothic
hicup
hic-c
hic
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
mictadlo
▴ 10
0
votes
1
reply
928
views
Error in scanBam(bam_fn) : could not find function "scanBam"
hic
diffhic
gothic
hicup
hic-c
5.5 years ago
mictadlo
▴ 10
3
votes
2
replies
2.4k
views
Best way to get HiCUP-mapped Hi-C data into diffHiC
hicup
hi-c
diffhic
homer
7.0 years ago • updated 6.9 years ago
e.jacobson
▴ 10
4 results • Page
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Answer: Behaviour of featureCounts when quantifying multi-mapping reads
by
Yang Liao
▴ 400
Both `v1.5.0` and `v1.6.4` versions are very old. I suggest upgrading to `v2.0.6` (the latest version). There was a change regarding the `…
Comment: Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() fr
by
Ozan
• 0
Sounds good. Thanks again!
Comment: Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() fr
by
James W. MacDonald
66k
Ah, ok. Doesn't really matter though. Try using `UniProt.ws`.
Comment: Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() fr
by
Ozan
• 0
I believe my `NCBI.sqlite` database is located in the same directory, but for some reason it seems to be empty. Even in the File explorer i…
Comment: Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() fr
by
James W. MacDonald
66k
You have to do that in the directory that contains your NCBI.sqlite database. ``` > library(RSQLite) > con <- dbConnect(SQLite(), "thisfil…
Votes
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Comment: Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() fr
Comment: Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() fr
Comment: Error: no such table: main.gene2pubmed when running makeOrgPackageFromNCBI() fr
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
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