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MOSAiCS User Group

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Aarthi Ramakrishnan

1/26/24

Processing files for rn6 and rn7

Hello, 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 rn7

Hello, 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

4/8/20

I have some PET ChIP data that I'm trying to use in MOSAiCS to call peaks. I've aligned it

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I 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 peaks

Thanks 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 peaks

Thanks 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 size

Hi, 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 size

Hi, I was wondering if you could please share M, GC and N files for binSize= 70 bp (and/or 69bp?),

5/9/17

4/26/17

Error in system(CMD, intern = TRUE, ignore.stderr = TRUE) : 'perl' not found

Hi 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 found

Hi 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 size

Hi Jinrui, In general, bin size has only limited effects on the results, essentially spatial

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fragment size and bin size

Hi 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 upgrade

Hi 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 upgrade

Hi Dongjun, This problem is back again at least since 6/2015. There are quite a few posts about this

4/1/17

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

1/13/17

M, GC and N files for 750bp

Hi, 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 750bp

Hi, 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 chromosomes

Thanks 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 chromosomes

Thanks 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 constructBin

Hello 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 constructBin

Hello 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 count

Hi 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 count

Hi Blanca, Those plots show the relationship between mean ChIP tag counts vs. mappability or GC

6/18/15

4/26/15

mosaicsFit - rlm failed to converge

Hello 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 converge

Hello Long since this group has been active, but ill try anyway. Im trying to use mosaics, but i get

4/26/15

12/13/14

preprocessed data sets for hg19 and mm10

Hi 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 mm10

Hi 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 galGal4

Hi 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 galGal4

Hi Adira, Overall, what you did looks OK to me. In this case, you might need to directly contact

8/28/14

8/18/14

Aberrations in peak calling for deeply sequenced replicate data sets

Dear 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 sets

Dear MOSAiCS users, I have a quick question about an aberration I'm dealing with in calling peaks

8/18/14

7/17/14

preprocessed GC and mappability scores for hg19

Hi, 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 hg19

Hi, 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 bug

Hi, Thanks for the package, Recently I have been using the package and after running the following

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A small code bug

Hi, Thanks for the package, Recently I have been using the package and after running the following

6/10/14

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 bins

Hi Sarah, It is great to hear that your problem is fixed! Now, please enjoy our MOSAiCS software! :)

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Error reading in bins

Hi 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+EBV

I 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+EBV

I 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 error

Hi 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 error

Hi 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 needed

Hi 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 needed

Hi 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 output

Hi Sharad, Please use constructBins() function in the mosaics package instead of the perl script

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perl script to preprocess eland output

Hi Sharad, Please use constructBins() function in the mosaics package instead of the perl script

5/31/13

12/19/12

Query using Mosaics

Greetings. 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 Mosaics

Greetings. 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 files

Hi Sigrid, mosaics does not support bam file formats as its direct input but it supports sam file

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Mosaics for bam files

Hi Sigrid, mosaics does not support bam file formats as its direct input but it supports sam file

9/29/12

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