User: rbronste

gravatar for rbronste
rbronste340
Reputation:
340
Status:
Trusted
Location:
Last seen:
5 days, 18 hours ago
Joined:
3 years, 1 month ago
Email:
r************@gmail.com

Posts by rbronste

<prev • 270 results • page 1 of 27 • next >
0
votes
1
answer
106
views
1
answers
Comment: C: grep sorting question
... This does seem to work in terms of ordering the sites however the gencode list has 54K rows and my gene list has 14k but I get a final tally of 140K rows. Is that due to alternate promoters? ...
written 6 days ago by rbronste340
0
votes
1
answer
106
views
1
answers
Comment: C: grep sorting question
... Yes thats right, Im going to use the resulting BED file for a heatmap where the descending order is important. ...
written 6 days ago by rbronste340
0
votes
1
answer
106
views
1
answers
Comment: C: grep sorting question
... The purpose is simple. The genes are in an order of descending normalized signal strength in the txt file, I would like the same in the TSS interval file for those specific genes. ...
written 6 days ago by rbronste340
0
votes
1
answer
106
views
1
answers
Comment: C: grep sorting question
... Just added the `head` output ...
written 6 days ago by rbronste340
3
votes
1
answer
106
views
1
answer
grep sorting question
... Hi I have the following code: grep -w -F -i -f gene_list.txt gencode.vM18.promoters.bed > gene_list_promoters.bed head gene_list.txt Rn45s Malat1 Sptbn1 head gencode.vM18.promoters.bed chr1 3071252 3075252 ENSMUSG00000102693.1 . + ...
grep awk sed unix bash written 6 days ago by rbronste340 • updated 6 days ago by RamRS25k
0
votes
1
answer
2.4k
views
1
answers
Comment: C: multiple bed - merge regions IF overlapping more than xx percent of size
... So I have the following code: N=6 bedops --everything \ | bedmap --echo-map --fraction-both 0.1 - \ | awk -vN=${N} '(split($0, a, ";") == N)' - \ | sed 's/\;/\n/g' - \ | sort-bed - \ | uniq - \ | bedops --merge - \ > answer1.bed I ...
written 11 days ago by rbronste340
0
votes
0
answers
76
views
0
answers
ggplot2 loess curve application to 2 dataframes
... Hi I am trying to create a loess curve for two dataframes within the same plot with a **different** span value for each, not sure exactly how to go about that, here is my code thus far which adds the loess curve to both sets of data but with the **same** span value. Thanks. ggplot(dplyr::bind_r ...
ggplot2 ggplot written 21 days ago by rbronste340
0
votes
1
answer
115
views
1
answers
Comment: C: EnhancedVolcano R pdf export size
... Thanks, very helpful! So my input table in this instance is a DESeqDataSet, would you still use sample() or seq() in that case? I have about 325K variables and would def be able to remove 50% within certain FC and pval constraints, probably FC < 2 and pval > .5 ...
written 23 days ago by rbronste340
5
votes
1
answer
115
views
1
answer
EnhancedVolcano R pdf export size
... Hi, I was wondering if anyone knew a way to make the export of pdfs from EnhancedVolcano significantly smaller in terms of file size for plots containing many points (over 100K). Right now they are like 4mb after externally reducing the size of the pdf before manipulating it in Illustrator which i ...
R enhancedvolcano volcano plot written 23 days ago by rbronste340 • updated 23 days ago by zx87549.0k
0
votes
0
answers
98
views
0
answers
Comment: C: Difficult filtering scenario of BED file
... Column B is the start coordinate yes but I don't want the distance between B and C to be 500, I want distance of adjoining starting intervals in column B to not exceed 500 while being limited to some range in column 4. ...
written 25 days ago by rbronste340

Latest awards to rbronste

Popular Question 29 days ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Removing PCR duplicates - fastq or BAM?
Popular Question 3 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 3 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 4 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 4 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 5 months ago, created a question with more than 1,000 views. For Figure quality browser tracks
Popular Question 5 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 6 months ago, created a question with more than 1,000 views. For Figure quality browser tracks
Popular Question 8 months ago, created a question with more than 1,000 views. For Removing PCR duplicates - fastq or BAM?
Great Question 9 months ago, created a question with more than 5,000 views. For Trouble installing R package Cairo
Popular Question 9 months ago, created a question with more than 1,000 views. For Removing PCR duplicates - fastq or BAM?
Popular Question 9 months ago, created a question with more than 1,000 views. For Comparing open chromatin data to ChromHMM model
Popular Question 9 months ago, created a question with more than 1,000 views. For FIMO GFF output to standard BED
Popular Question 9 months ago, created a question with more than 1,000 views. For Figure quality browser tracks
Popular Question 9 months ago, created a question with more than 1,000 views. For Table browser +/- 2Kb of TSS export
Popular Question 11 months ago, created a question with more than 1,000 views. For Removing PCR duplicates - fastq or BAM?
Popular Question 13 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Student 14 months ago, asked a question with at least 3 up-votes. For MEME vs. HOMER for de novo and known Motif finding
Popular Question 15 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 16 months ago, created a question with more than 1,000 views. For Blacklisted regions for mm10
Popular Question 16 months ago, created a question with more than 1,000 views. For Duplicates in ATAC-seq data

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1717 users visited in the last hour