Moderator: PoGibas
PoGibas ♦ 4.7k
- Reputation:
- 4,730
- Status:
- Trusted
- Location:
- Vilnius
- Twitter:
- PoGibas
- Last seen:
- 3 months, 4 weeks ago
- Joined:
- 6 years, 8 months ago
- Email:
- p***********@gmail.com
PhD candidate - newbie in bioinformatics, interested in genome architecture & mining big data.
Posts by PoGibas
<prev
• 560 results •
page 1 of 56 •
next >
1
vote
1
answer
557
views
1
answers
Comment:
C: problems in data frame
... You forgot to `library(data.table)`. BTW, why do you need `as.data.frame` on `data.table` object (`fread` output)? Why not to:
data.table(gene = fread("gene.txt"),
meth = fread("meth.txt")) ...
written 15 months ago by
PoGibas ♦ 4.7k
1
vote
1
answer
838
views
1
answers
... All you need is original [bedtools intersect][1] and linux `join` command.
Algorithm goes like that:
for i in cellLineBed {
# you need wao to get all reports in -a
# possible to overcome this with linux join
bedtoolsIntersect -a originalBedFile -b ${i}_cellLineBed -wao ...
written 16 months ago by
PoGibas ♦ 4.7k
2
votes
0
answers
1.2k
views
0
answers
... Few comments:
- For "STRG" prefix read stringtie manual
- If you want to estimate the abundance of given reference transcripts (use `-e` flag with `-G`)
...
written 17 months ago by
PoGibas ♦ 4.7k
1
vote
1
answer
827
views
1
answer
... I have used StringTie on mice RNA-seq data. StringTie was run with parameters given in [Nature paper](http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html). Reference gtf annotation was downloaded from the Gencode Genes.
Most of the transcripts in the reference annotation have very ...
2
votes
1
answer
611
views
1
answers
... I would use `bedtools getfasta`. You will need:
- Arabidobsis genome (fasta format)
- Regions of interest (bed format - you already have this)
...
written 18 months ago by
PoGibas ♦ 4.7k
1
vote
1
answer
710
views
1
answers
Comment:
C: Finding the error in the code
... R tells you where the error is... Did you read the message? ...
written 18 months ago by
PoGibas ♦ 4.7k
0
votes
1
answer
714
views
1
answers
Comment:
C: possion distribution of ChIP-seq
... You never know: https://www.ncbi.nlm.nih.gov/pubmed/?term=possion
"Multivariate possion regression analysis was applied ..." :) ...
written 18 months ago by
PoGibas ♦ 4.7k
0
votes
2
answers
1.1k
views
2
answers
... What is end of the contig? 1kb? ...
written 19 months ago by
PoGibas ♦ 4.7k
0
votes
1
answer
703
views
1
answers
... What was the result of bioconductor command? ...
written 19 months ago by
PoGibas ♦ 4.7k
0
votes
4
answers
638
views
4
answers
Comment:
C: Read a text file into a list
... I still don't know if this is the thing you wanted to do? ...
written 19 months ago by
PoGibas ♦ 4.7k
Latest awards to PoGibas
Great Question
8 months ago,
created a question with more than 5,000 views.
For Sort Multiple Fasta Numerically
Popular Question
11 months ago,
created a question with more than 1,000 views.
For GC content in bilsulfite converted library
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Sort Multiple Fasta Numerically
Popular Question
13 months ago,
created a question with more than 1,000 views.
For Sort Multiple Fasta Numerically
Commentator
13 months ago,
created a comment with at least 3 up-votes.
For C: Ask For A Script To Carry Out Reverse Complement Of Dna Sequence
Appreciated
13 months ago,
created a post with more than 5 votes.
For C: Ask For A Script To Carry Out Reverse Complement Of Dna Sequence
Great Question
14 months ago,
created a question with more than 5,000 views.
For Bedtools "Segmentation Fault" While Working With Genome.Fa
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Pcr Primer In Highly Repetitive Region
Commentator
17 months ago,
created a comment with at least 3 up-votes.
For C: Ask For A Script To Carry Out Reverse Complement Of Dna Sequence
Good Answer
18 months ago,
created an answer that was upvoted at least 5 times.
For C: How to do coverage counting for each genomic position in R ?
Scholar
19 months ago,
created an answer that has been accepted.
For A: Bedtools intersect with minimum overlap required as a number
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Pcr Primer In Highly Repetitive Region
Scholar
20 months ago,
created an answer that has been accepted.
For A: Bedtools intersect with minimum overlap required as a number
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Pcr Primer In Highly Repetitive Region
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Blast2 Like Local Aligner
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Blast2 Like Local Aligner
Great Question
23 months ago,
created a question with more than 5,000 views.
For Counting N'S Within Fasta
Popular Question
23 months ago,
created a question with more than 1,000 views.
For Blast2 Like Local Aligner
Popular Question
24 months ago,
created a question with more than 1,000 views.
For Blast2 Like Local Aligner
Good Answer
24 months ago,
created an answer that was upvoted at least 5 times.
For C: How to do coverage counting for each genomic position in R ?
Popular Question
2.0 years ago,
created a question with more than 1,000 views.
For Blast2 Like Local Aligner
Popular Question
2.0 years ago,
created a question with more than 1,000 views.
For 7N Motif Search Over The Genome
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1835 users visited in the last hour