Moderator: PoGibas

gravatar for PoGibas
PoGibas4.8k
Reputation:
4,780
Status:
Trusted
Location:
Vilnius
Twitter:
PoGibas
Last seen:
1 month, 1 week ago
Joined:
7 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
677
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 23 months ago by PoGibas4.8k
1
vote
1
answer
1.3k
views
1
answers
Comment: C: Find overlapping coordinates between a bed file and multiple files in order and
... 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 24 months ago by PoGibas4.8k
2
votes
0
answers
1.7k
views
0
answers
Comment: C: Help regarding RNA-seq STRINGTIE pipeline and output
... 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 2.1 years ago by PoGibas4.8k
1
vote
1
answer
1.1k
views
1
answer
StringTie reports 0 coverage for all reference transcripts
... 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 ...
stringtie rna-seq written 2.2 years ago by PoGibas4.8k • updated 2.1 years ago by k.mooo10
2
votes
1
answer
830
views
1
answers
Answer: C: How to get arabidopsis sequences from genome coordinates
... I would use `bedtools getfasta`. You will need: - Arabidobsis genome (fasta format) - Regions of interest (bed format - you already have this) ...
written 2.2 years ago by PoGibas4.8k
1
vote
1
answer
946
views
1
answers
Comment: C: Finding the error in the code
... R tells you where the error is... Did you read the message? ...
written 2.2 years ago by PoGibas4.8k
0
votes
1
answer
928
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 2.2 years ago by PoGibas4.8k
0
votes
2
answers
1.7k
views
2
answers
Comment: C: search for low coverage regions on bam file
... What is end of the contig? 1kb? ...
written 2.2 years ago by PoGibas4.8k
0
votes
1
answer
956
views
1
answers
Comment: C: Is it impossible to install geneplotter in R version 3.3.2
... What was the result of bioconductor command? ...
written 2.3 years ago by PoGibas4.8k
0
votes
4
answers
789
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 2.3 years ago by PoGibas4.8k

Latest awards to PoGibas

Popular Question 4 months ago, created a question with more than 1,000 views. For GC content in bilsulfite converted library
Great Question 4 months ago, created a question with more than 5,000 views. For Sort Multiple Fasta Numerically
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Extract According To Row
Good Answer 4 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 4 months ago, created a question with more than 10,000 views. For Counting N'S Within Fasta
Good Question 4 months ago, asked a question that was upvoted at least 5 times. For Picking Random Genomic Positions
Appreciated 12 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 12 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
Popular Question 19 months ago, created a question with more than 1,000 views. For GC content in bilsulfite converted library
Popular Question 20 months ago, created a question with more than 1,000 views. For Sort Multiple Fasta Numerically
Popular Question 22 months ago, created a question with more than 1,000 views. For Sort Multiple Fasta Numerically
Appreciated 22 months ago, created a post with more than 5 votes. For C: Ask For A Script To Carry Out Reverse Complement Of Dna Sequence
Commentator 22 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
Great Question 22 months ago, created a question with more than 5,000 views. For Bedtools "Segmentation Fault" While Working With Genome.Fa
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Extract According To Row
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Pcr Primer In Highly Repetitive Region
Commentator 2.1 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 2.2 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 ?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Extract According To Row
Scholar 2.3 years ago, created an answer that has been accepted. For A: Bedtools intersect with minimum overlap required as a number
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Pcr Primer In Highly Repetitive Region
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Extract According To Row
Scholar 2.4 years ago, created an answer that has been accepted. For A: Bedtools intersect with minimum overlap required as a number
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Pcr Primer In Highly Repetitive Region

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 544 users visited in the last hour