User: a.rex

gravatar for a.rex
a.rex170
Reputation:
170
Status:
Trusted
Location:
Last seen:
1 week, 3 days ago
Joined:
2 years, 4 months ago
Email:
a************@st-annes.ox.ac.uk

Posts by a.rex

<prev • 121 results • page 1 of 13 • next >
1
vote
0
answers
92
views
0
answers
How can I get Kimura distances for individual loci from my align.fa file from RepeatMasker
... I have a set of transcripts which I have run through RepeatMasker. I have an output align file which I want to parse to get Kimura distances for individual loci? Does anyone have a script to do this? ...
repeatmasker written 6 weeks ago by a.rex170 • updated 11 days ago by Biostar ♦♦ 20
2
votes
1
answer
159
views
1
answer
Using FeatureCounts for ChIP-seq normalised files?
... I have a set of bed intervals (that correspond to genomic regions of open ATAC NFR regions). I also have ChIP-seq bigwig files for a histone mark that have been normalised to input with Deeptools2' bamCompare. I would like to use FeaturesCount to count the number of normalised reads in each interval ...
deeptools chip-seq written 7 weeks ago by a.rex170 • updated 7 weeks ago by Devon Ryan87k
0
votes
1
answer
188
views
1
answers
Comment: C: Trouble with danpos2 installation - can anyone help?
... This was the error when using the conda link above. PackagesNotFoundError: The following packages are not available from current channels: - danpos - samtools ...
written 7 weeks ago by a.rex170
0
votes
1
answer
188
views
1
answers
Comment: C: Trouble with danpos2 installation - can anyone help?
... Nope, this doesn't work ...
written 7 weeks ago by a.rex170
0
votes
0
answers
129
views
0
answers
Can I use deeptools to calculate nucleosome positions?
... I have some ATAC-data that I have separated into fragments less than 100bp, and fragment >150bp. Can I normalise them to each other (i.e. the 150 bam normalised against the <100 bam) to get my potential nucleosome reads? Can I do this in deep tools. Nucleoatac has proven to be quiet conservati ...
deeptools atac written 7 weeks ago by a.rex170
5
votes
1
answer
188
views
5 follow
1
answer
Trouble with danpos2 installation - can anyone help?
... I have used conda to install both R and rpy2. When I try to run python danpos.py -h to install the danpos package I get the following error: Traceback (most recent call last): File "danpos.py", line 6, in from functions import danpos File "/path/danpos-2.2.2/functions.py", ...
installation python danpos written 7 weeks ago by a.rex170 • updated 7 weeks ago by h.mon22k
0
votes
0
answers
113
views
0
answers
Performing differential binding analyses between ChIP samples using Deeptools (SES method normalization)
... I have 2 conditions under which I performed ChIP, each with 3 replicates. I want to perform differential binding analyses between them. I generally get a coverage file using the bamCoverage tool in deep tools (with the SES method) - this allows me to visualise my ChIP signal tracks and compare. But ...
chip-seq written 8 weeks ago by a.rex170
0
votes
0
answers
212
views
0
answers
Comment: C: How can I correlate ATAC-seq peak signal with enhancer ChIP-seq mark signal (H3K
... Yes, I realise that it can be a feature of both active and poised enhancers. https://www.abcam.com/epigenetics/histone-modifications-and-where-to-find-them ...
written 8 weeks ago by a.rex170
1
vote
0
answers
212
views
0
answers
How can I correlate ATAC-seq peak signal with enhancer ChIP-seq mark signal (H3K4me1)?
... I have a set of ATAC-peaks which I would like to correlate, somehow, with the level of H3K4me1 flanking these peaks? This is because, H3K4me1 is a well known marker for active enhancers. Would people recommend to do a Pearson correlation between ATAC-peaks read level and H3K4me1 read level flanking ...
chip atac written 8 weeks ago by a.rex170
0
votes
0
answers
217
views
0
answers
Comment: C: Explaining PCA plots made from BigWig coverage files in DeepTools
... what does this do? I don't understand what transpose does to the information? ...
written 8 weeks ago by a.rex170

Latest awards to a.rex

Voter 7 weeks ago, voted more than 100 times.
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Fetching NCBI ID for a list of species?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Fetching NCBI ID for a list of species?
Centurion 12 weeks ago, created 100 posts.
Popular Question 3 months ago, created a question with more than 1,000 views. For Issues installing bcl2fastq?
Popular Question 3 months ago, created a question with more than 1,000 views. For Fetching NCBI ID for a list of species?
Popular Question 5 months ago, created a question with more than 1,000 views. For parse error with samtools
Popular Question 5 months ago, created a question with more than 1,000 views. For Issues installing bcl2fastq?
Student 5 months ago, asked a question with at least 3 up-votes. For mapping reads to repetitive elements in genome?
Popular Question 7 months ago, created a question with more than 1,000 views. For createRepeatLandscape in RepeatMasker
Popular Question 12 months ago, created a question with more than 1,000 views. For Issues installing bcl2fastq?
Supporter 22 months ago, voted at least 25 times.
Student 2.0 years ago, asked a question with at least 3 up-votes. For mapping reads to repetitive elements in genome?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2308 users visited in the last hour