Moderator: PoGibas
PoGibas ♦ 4.8k
- Reputation:
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- Vilnius
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- PoGibas
- Last seen:
- 9 months, 4 weeks ago
- Joined:
- 8 years ago
- Email:
- p***********@gmail.com
PhD candidate - newbie in bioinformatics, interested in genome architecture & mining big data.
Posts by PoGibas
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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 2.7 years ago by
PoGibas ♦ 4.8k
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... 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 2.7 years ago by
PoGibas ♦ 4.8k
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... 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 2.8 years ago by
PoGibas ♦ 4.8k
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... 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
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... I would use `bedtools getfasta`. You will need:
- Arabidobsis genome (fasta format)
- Regions of interest (bed format - you already have this)
...
written 2.9 years ago by
PoGibas ♦ 4.8k
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Comment:
C: Finding the error in the code
... R tells you where the error is... Did you read the message? ...
written 2.9 years ago by
PoGibas ♦ 4.8k
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1.1k
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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 2.9 years ago by
PoGibas ♦ 4.8k
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... What is end of the contig? 1kb? ...
written 3.0 years ago by
PoGibas ♦ 4.8k
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1.1k
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... What was the result of bioconductor command? ...
written 3.0 years ago by
PoGibas ♦ 4.8k
0
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4
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898
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4
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Comment:
C: Read a text file into a list
... I still don't know if this is the thing you wanted to do? ...
written 3.0 years ago by
PoGibas ♦ 4.8k
Latest awards to PoGibas
Popular Question
12 months ago,
created a question with more than 1,000 views.
For GC content in bilsulfite converted library
Great Question
12 months ago,
created a question with more than 5,000 views.
For Sort Multiple Fasta Numerically
Good Answer
12 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
12 months ago,
created a question with more than 10,000 views.
For Counting N'S Within Fasta
Good Question
13 months ago,
asked a question that was upvoted at least 5 times.
For Picking Random Genomic Positions
Appreciated
20 months 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
20 months ago,
created a question with more than 1,000 views.
For GC content in bilsulfite converted library
Great Question
2.1 years ago,
created a question with more than 5,000 views.
For Sort Multiple Fasta Numerically
Popular Question
2.3 years ago,
created a question with more than 1,000 views.
For GC content in bilsulfite converted library
Popular Question
2.4 years ago,
created a question with more than 1,000 views.
For Sort Multiple Fasta Numerically
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For Sort Multiple Fasta Numerically
Appreciated
2.5 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
2.5 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
2.6 years ago,
created a question with more than 5,000 views.
For Bedtools "Segmentation Fault" While Working With Genome.Fa
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Pcr Primer In Highly Repetitive Region
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
Good Answer
2.9 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
3.0 years ago,
created an answer that has been accepted.
For A: Bedtools intersect with minimum overlap required as a number
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For Pcr Primer In Highly Repetitive Region
Scholar
3.1 years ago,
created an answer that has been accepted.
For A: Bedtools intersect with minimum overlap required as a number
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For Pcr Primer In Highly Repetitive Region
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