MOSAiCS User Group - Google Groups (original) (raw)
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Aarthi Ramakrishnan
1/26/24
Processing files for rn6 and rn7Hello, Would MOSAiCS be able to provide preprocessing files for rn6 and rn7? Would be super helpful.
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Processing files for rn6 and rn7Hello, Would MOSAiCS be able to provide preprocessing files for rn6 and rn7? Would be super helpful.
1/26/24
Seung Jin Park, Dedeepya Vaka2
8/17/21
Error in fitting step [singular fits are not implemented in 'rlm']Hi, I am getting the same error message. Can you please let m eknow how you resolved On Monday,
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Error in fitting step [singular fits are not implemented in 'rlm']Hi, I am getting the same error message. Can you please let m eknow how you resolved On Monday,
8/17/21
Kevin Myers
4/8/20
PET Data ErrorI have some PET ChIP data that I'm trying to use in MOSAiCS to call peaks. I've aligned it
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PET Data ErrorI have some PET ChIP data that I'm trying to use in MOSAiCS to call peaks. I've aligned it
4/8/20
Rajat Singhania, Dongjun Chung3
5/19/17
combining replicates to call peaksThanks Dongjun, that's good to know. Rajat On Thursday, May 18, 2017 at 7:01:44 PM UTC-4, Dongjun
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combining replicates to call peaksThanks Dongjun, that's good to know. Rajat On Thursday, May 18, 2017 at 7:01:44 PM UTC-4, Dongjun
5/19/17
mmo...@gmail.com
5/9/17
M, GC and N files for 70 bp fragment sizeHi, I was wondering if you could please share M, GC and N files for binSize= 70 bp (and/or 69bp?),
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M, GC and N files for 70 bp fragment sizeHi, I was wondering if you could please share M, GC and N files for binSize= 70 bp (and/or 69bp?),
5/9/17
tarek Mohamed
4/26/17
Error in system(CMD, intern = TRUE, ignore.stderr = TRUE) : 'perl' not foundHi All, I am trying to use mosaics package to call peaks for my chip-seq experiment. however I got an
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Error in system(CMD, intern = TRUE, ignore.stderr = TRUE) : 'perl' not foundHi All, I am trying to use mosaics package to call peaks for my chip-seq experiment. however I got an
4/26/17
Jin-Rui Xu, Dongjun Chung2
4/8/17
fragment size and bin sizeHi Jinrui, In general, bin size has only limited effects on the results, essentially spatial
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fragment size and bin sizeHi Jinrui, In general, bin size has only limited effects on the results, essentially spatial
4/8/17
John, … Dongjun Chung7
4/8/17
constructBin error (due to bowtie2 format?)Hi all, Some of them seem to be the errors that exist in older versions of mosaics package and they
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constructBin error (due to bowtie2 format?)Hi all, Some of them seem to be the errors that exist in older versions of mosaics package and they
4/8/17
Branden Timm, … Jin-Rui Xu4
4/1/17
generateWig errors after upgradeHi Dongjun, This problem is back again at least since 6/2015. There are quite a few posts about this
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generateWig errors after upgradeHi Dongjun, This problem is back again at least since 6/2015. There are quite a few posts about this
4/1/17
Peng
1/16/17
preprocessing M, GC, and N files for hg38?Hi Dongjun, I am wondering if MOSAiCS could provide preprocessing files for hg38? I believe hg38
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preprocessing M, GC, and N files for hg38?Hi Dongjun, I am wondering if MOSAiCS could provide preprocessing files for hg38? I believe hg38
1/16/17
Siddhant Jain
1/13/17
M, GC and N files for 750bpHi, I was wondering if you could please share M, GC and N files for binSize= 750 bp. I am calling
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M, GC and N files for 750bpHi, I was wondering if you could please share M, GC and N files for binSize= 750 bp. I am calling
1/13/17
Oleg Moskvin, Peng3
3/26/16
"Number found where operator expected"Hi Oleg, I got the similar error message as yours. I think it is probably because mosaics cannot find
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"Number found where operator expected"Hi Oleg, I got the similar error message as yours. I think it is probably because mosaics cannot find
3/26/16
julie dubois, … Aayushi Jain8
2/13/16
readBins with M, GC and N score for all chromosomesThanks again ! -Aayushi Aayushi Jain B.Tech, M.Tech (Biochemical Engg), IIT Delhi Graduate Student,
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readBins with M, GC and N score for all chromosomesThanks again ! -Aayushi Aayushi Jain B.Tech, M.Tech (Biochemical Engg), IIT Delhi Graduate Student,
2/13/16
Sean McIlwain, Dongjun Chung2
1/26/16
ftp://ftp.cs.wisc.edu/pub/users/kelesgroup/MOSAiCS/ not available?Hi Sean, I just checked the ftp server and it seems that all the files can be accessed properly. Can
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ftp://ftp.cs.wisc.edu/pub/users/kelesgroup/MOSAiCS/ not available?Hi Sean, I just checked the ftp server and it seems that all the files can be accessed properly. Can
1/26/16
John, Dongjun Chung4
6/23/15
Error with constructBinHello again, I get an error message when using a sam file that looks like the header (see below) is
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Error with constructBinHello again, I get an error message when using a sam file that looks like the header (see below) is
6/23/15
Blanca Tirado Cobos, Dongjun Chung2
6/18/15
Plot: Mappability/GC content score vs. Mean ChIP tag countHi Blanca, Those plots show the relationship between mean ChIP tag counts vs. mappability or GC
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Plot: Mappability/GC content score vs. Mean ChIP tag countHi Blanca, Those plots show the relationship between mean ChIP tag counts vs. mappability or GC
6/18/15
Jesper Grud
4/26/15
mosaicsFit - rlm failed to convergeHello Long since this group has been active, but ill try anyway. Im trying to use mosaics, but i get
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mosaicsFit - rlm failed to convergeHello Long since this group has been active, but ill try anyway. Im trying to use mosaics, but i get
4/26/15
Peng2
12/13/14
preprocessed data sets for hg19 and mm10Hi Dongjun, Please ignore my previous request. I have found a way to resolve it. Best, Peng On Friday
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preprocessed data sets for hg19 and mm10Hi Dongjun, Please ignore my previous request. I have found a way to resolve it. Best, Peng On Friday
12/13/14
Adira Mollari, Dongjun Chung2
8/28/14
Mappability tracks for danRer7 and galGal4Hi Adira, Overall, what you did looks OK to me. In this case, you might need to directly contact
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Mappability tracks for danRer7 and galGal4Hi Adira, Overall, what you did looks OK to me. In this case, you might need to directly contact
8/28/14
Sara Knaack
8/18/14
Aberrations in peak calling for deeply sequenced replicate data setsDear MOSAiCS users, I have a quick question about an aberration I'm dealing with in calling peaks
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Aberrations in peak calling for deeply sequenced replicate data setsDear MOSAiCS users, I have a quick question about an aberration I'm dealing with in calling peaks
8/18/14
Anna
7/17/14
preprocessed GC and mappability scores for hg19Hi, Maybe I am overlooking something obvious, but I can't find the preprocessed files for GC
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preprocessed GC and mappability scores for hg19Hi, Maybe I am overlooking something obvious, but I can't find the preprocessed files for GC
7/17/14
DJEKIDEL MOHAMED NADHIR
6/10/14
A small code bugHi, Thanks for the package, Recently I have been using the package and after running the following
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A small code bugHi, Thanks for the package, Recently I have been using the package and after running the following
6/10/14
Lorena Pantano
5/23/14
GC, M and N files for mm10?Hi, I would like to use your package, but I want to run my data using mm10 since it is more complete
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GC, M and N files for mm10?Hi, I would like to use your package, but I want to run my data using mm10 since it is more complete
5/23/14
Sarah Carl, Dongjun Chung10
5/15/14
Error reading in binsHi Sarah, It is great to hear that your problem is fixed! Now, please enjoy our MOSAiCS software! :)
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Error reading in binsHi Sarah, It is great to hear that your problem is fixed! Now, please enjoy our MOSAiCS software! :)
5/15/14
Kyle McChesney, Dongjun Chung7
5/6/14
Generating bin-level GC, N, Mapability for HG19+EBVI looked through the old threads and found people having similar issues. I tried doing and IO fit,
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Generating bin-level GC, N, Mapability for HG19+EBVI looked through the old threads and found people having similar issues. I tried doing and IO fit,
5/6/14
Sara Knaack, Dongjun Chung2
4/16/14
Odd peak calling errorHi Sara, Thanks for your interest in MOSAiCS and I am sorry for the inconvenience due to the errors.
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Odd peak calling errorHi Sara, Thanks for your interest in MOSAiCS and I am sorry for the inconvenience due to the errors.
4/16/14
eddieasalinas, … Dongjun Chung7
12/23/13
Error in while (abs(logLik[iter] - logLik[iter - 1]) > eps & iter < 10) { : missing value where TRUE/FALSE neededHi Sara, analysisType="TS" works differently from analysisType="IO" only for the
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Error in while (abs(logLik[iter] - logLik[iter - 1]) > eps & iter < 10) { : missing value where TRUE/FALSE neededHi Sara, analysisType="TS" works differently from analysisType="IO" only for the
12/23/13
tim, … Dongjun Chung11
5/31/13
perl script to preprocess eland outputHi Sharad, Please use constructBins() function in the mosaics package instead of the perl script
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perl script to preprocess eland outputHi Sharad, Please use constructBins() function in the mosaics package instead of the perl script
5/31/13
nafeesa mazhar
12/19/12
Query using MosaicsGreetings. I have two two types of binding regions say A n B in mcf7 cell line A type binding regions
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Query using MosaicsGreetings. I have two two types of binding regions say A n B in mcf7 cell line A type binding regions
12/19/12
SR, Dongjun Chung2
9/29/12
Mosaics for bam filesHi Sigrid, mosaics does not support bam file formats as its direct input but it supports sam file
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Mosaics for bam filesHi Sigrid, mosaics does not support bam file formats as its direct input but it supports sam file
9/29/12