User: bioinfc37

gravatar for bioinfc37
bioinfc3730
Reputation:
30
Status:
New User
Location:
Last seen:
8 months ago
Joined:
1 year, 9 months ago
Email:
b********@gmail.com

Posts by bioinfc37

<prev • 10 results • page 1 of 1 • next >
8
votes
2
answers
388
views
5 follow
2
answers
Validating ChIP-seq peak-calling output across replicates
... In general, I would like to validate my ChIP-seq output from MACS2. My ChIP-seq dataset contains libraries that are not pure technical replicates -- the biological sample (1 tube) was divided in three samples (three tubes) for sequencing. The variation between samples is likely due to the sequencer. ...
chip-seq written 8 months ago by bioinfc3730 • updated 8 months ago by Sentinel15690
2
votes
1
answer
275
views
1
answer
Comprehensive annotations for rat
... Seeking the most comprehensive database for the rat models (rn5) or a pipeline to generate a richer annotation for this organism. ...
annotation written 8 months ago by bioinfc3730 • updated 8 months ago by Denise - Open Targets4.0k
1
vote
0
answers
327
views
0
answers
Enhancer regions for rn5
... Seeking a reproducible database for `rn5` enhancer regions or a protocol that I could use as a reference -- any leads? Thanks in advance! ...
enhancer rn5 written 11 months ago by bioinfc3730
0
votes
0
answers
357
views
0
answers
Help tag sequencing output
... I have data from HELP tag sequencing The output looks as follows: > 1 chr1 350 3.5467 3.5918 > 2 chr1 20066 0.0000 2.6648 > 3 chr1 27464 0.0000 2.9885 > 4 chr1 29783 0.0000 0.5977 > 7 chr1 32795 0.0000 0.8966 > 8 chr1 33137 0.0000 14.3449 > 19 chr1 43680 0.0000 0.8966 & ...
sequencing written 17 months ago by bioinfc3730
0
votes
0
answers
428
views
0
answers
Comment: C: All possible predicted RNA in mm9 genome
... To state another way what I meant: A whole genome *in-silico* prediction of all possible sub-sequences of DNA that would form a secondary structure. ...
written 17 months ago by bioinfc3730
1
vote
0
answers
428
views
0
answers
All possible predicted RNA in mm9 genome
... Seeking a database of all possible predicted RNA in the entire mm9 genome. mfold will do this but has a 9000 base limit. I'm sure I can't be the first one who would like to browse the output of all possible predicted RNA structures from the genome including intronic sequences as a database where I ...
mm9 mouse rna genome written 17 months ago by bioinfc3730
1
vote
1
answer
454
views
1
answer
Retrieve Gene Annotations using BSgenome
... I have a matrix that consists of gene names. What is the most efficient method to retrieve the gene annotations using the BSgenome.Rnorvegicus.UCSC.rn5 package. Example of matrix: Oxtr Ebf2 Ppp1r1a Kcnc3 Thanks in advance ...
R written 19 months ago by bioinfc3730 • updated 19 months ago by mastal5111.7k
0
votes
1
answer
832
views
1
answers
Comment: C: Merge RNA-seq genelist with logFC with Chip-seq peaks
... Merge peaks or find intersecting regions between the peaks of the Chip-seq data and also the genelist. ...
written 20 months ago by bioinfc3730
4
votes
1
answer
832
views
1
answer
Merge RNA-seq genelist with logFC with Chip-seq peaks
... I have a genelist with RNA-seq expression + logFC and etc. I also have Chip-seq peaks, how do I merge these two very different data sets? Thanks! ...
chip-seq rna-seq written 20 months ago by bioinfc3730 • updated 20 months ago by vchris_ngs4.0k
2
votes
1
answer
542
views
1
answer
Rat rn5 GTF format
... Seeking a link to the Rat (rn5) "_RefSeq_Gene_UCSC.gtf format; cannot find it on UCSC . Does this file exist? ...
gene written 20 months ago by bioinfc3730 • updated 20 months ago by Dan D6.2k

Latest awards to bioinfc37

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 952 users visited in the last hour