Moderator: PoGibas
PoGibas ♦ 4.7k
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- PoGibas
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- Joined:
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- 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 19 months ago by
PoGibas ♦ 4.7k
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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 20 months ago by
PoGibas ♦ 4.7k
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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 21 months ago by
PoGibas ♦ 4.7k
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986
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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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1
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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 22 months ago by
PoGibas ♦ 4.7k
1
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1
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828
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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 22 months ago by
PoGibas ♦ 4.7k
0
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1
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828
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1
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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 22 months ago by
PoGibas ♦ 4.7k
0
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2
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1.4k
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2
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... What is end of the contig? 1kb? ...
written 23 months ago by
PoGibas ♦ 4.7k
0
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1
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830
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... What was the result of bioconductor command? ...
written 23 months ago by
PoGibas ♦ 4.7k
0
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4
answers
711
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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 23 months ago by
PoGibas ♦ 4.7k
Latest awards to PoGibas
Good Question
14 days ago,
asked a question that was upvoted at least 5 times.
For Picking Random Genomic Positions
Popular Question
7 months ago,
created a question with more than 1,000 views.
For GC content in bilsulfite converted library
Appreciated
7 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
12 months ago,
created a question with more than 5,000 views.
For Sort Multiple Fasta Numerically
Popular Question
15 months ago,
created a question with more than 1,000 views.
For GC content in bilsulfite converted library
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Sort Multiple Fasta Numerically
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Sort Multiple Fasta Numerically
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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
Appreciated
17 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
18 months ago,
created a question with more than 5,000 views.
For Bedtools "Segmentation Fault" While Working With Genome.Fa
Popular Question
21 months ago,
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For Pcr Primer In Highly Repetitive Region
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21 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
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22 months ago,
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For C: How to do coverage counting for each genomic position in R ?
Scholar
23 months ago,
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For A: Bedtools intersect with minimum overlap required as a number
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For Pcr Primer In Highly Repetitive Region
Scholar
2.0 years ago,
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For A: Bedtools intersect with minimum overlap required as a number
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For Counting N'S Within Fasta
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2.3 years ago,
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For C: How to do coverage counting for each genomic position in R ?
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