Moderator: PoGibas
PoGibas ♦ 4.8k
- Reputation:
- 4,810
- Status:
- Trusted
- Location:
- Vilnius
- Twitter:
- PoGibas
- Last seen:
- 1 year, 1 month ago
- Joined:
- 8 years, 4 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
829
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 3.0 years ago by
PoGibas ♦ 4.8k
1
vote
1
answer
2.0k
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 3.0 years ago by
PoGibas ♦ 4.8k
2
votes
0
answers
2.4k
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 3.1 years ago by
PoGibas ♦ 4.8k
1
vote
1
answer
1.5k
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
1.1k
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 3.3 years ago by
PoGibas ♦ 4.8k
1
vote
1
answer
1.3k
views
1
answers
Comment:
C: Finding the error in the code
... R tells you where the error is... Did you read the message? ...
written 3.3 years ago by
PoGibas ♦ 4.8k
0
votes
1
answer
1.2k
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 3.3 years ago by
PoGibas ♦ 4.8k
0
votes
2
answers
2.4k
views
2
answers
... What is end of the contig? 1kb? ...
written 3.3 years ago by
PoGibas ♦ 4.8k
0
votes
1
answer
1.3k
views
1
answers
... What was the result of bioconductor command? ...
written 3.3 years ago by
PoGibas ♦ 4.8k
0
votes
4
answers
956
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 3.3 years ago by
PoGibas ♦ 4.8k
Latest awards to PoGibas
Popular Question
16 months ago,
created a question with more than 1,000 views.
For GC content in bilsulfite converted library
Great Question
16 months ago,
created a question with more than 5,000 views.
For Sort Multiple Fasta Numerically
Good Answer
16 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 ?
Epic Question
16 months ago,
created a question with more than 10,000 views.
For Counting N'S Within Fasta
Good Question
17 months ago,
asked a question that was upvoted at least 5 times.
For Picking Random Genomic Positions
Appreciated
2.0 years ago,
created a post with more than 5 votes.
For C: Ask For A Script To Carry Out Reverse Complement Of Dna Sequence
Popular Question
2.0 years ago,
created a question with more than 1,000 views.
For GC content in bilsulfite converted library
Great Question
2.4 years ago,
created a question with more than 5,000 views.
For Sort Multiple Fasta Numerically
Popular Question
2.6 years ago,
created a question with more than 1,000 views.
For GC content in bilsulfite converted library
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Sort Multiple Fasta Numerically
Popular Question
2.9 years ago,
created a question with more than 1,000 views.
For Sort Multiple Fasta Numerically
Appreciated
2.9 years ago,
created a post with more than 5 votes.
For C: Ask For A Script To Carry Out Reverse Complement Of Dna Sequence
Commentator
2.9 years ago,
created a comment with at least 3 up-votes.
For C: Ask For A Script To Carry Out Reverse Complement Of Dna Sequence
Great Question
2.9 years ago,
created a question with more than 5,000 views.
For Bedtools "Segmentation Fault" While Working With Genome.Fa
Popular Question
3.2 years ago,
created a question with more than 1,000 views.
For Pcr Primer In Highly Repetitive Region
Commentator
3.2 years 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
3.2 years 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
3.3 years ago,
created an answer that has been accepted.
For A: Bedtools intersect with minimum overlap required as a number
Popular Question
3.4 years ago,
created a question with more than 1,000 views.
For Pcr Primer In Highly Repetitive Region
Scholar
3.4 years ago,
created an answer that has been accepted.
For A: Bedtools intersect with minimum overlap required as a number
Popular Question
3.4 years ago,
created a question with more than 1,000 views.
For Pcr Primer In Highly Repetitive Region
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 692 users visited in the last hour