Moderator: PoGibas

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PoGibas4.7k
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PoGibas
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2 months ago
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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 9 months ago by PoGibas4.7k
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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 9 months ago by PoGibas4.7k
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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 11 months ago by PoGibas4.7k
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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 12 months ago by PoGibas4.7k • updated 11 months ago by k.mooo10
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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 12 months ago by PoGibas4.7k
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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 12 months ago by PoGibas4.7k
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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 12 months ago by PoGibas4.7k
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Comment: C: search for low coverage regions on bam file
... What is end of the contig? 1kb? ...
written 13 months ago by PoGibas4.7k
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Comment: C: Is it impossible to install geneplotter in R version 3.3.2
... What was the result of bioconductor command? ...
written 13 months ago by PoGibas4.7k
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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 13 months ago by PoGibas4.7k

Latest awards to PoGibas

Popular Question 5 months ago, created a question with more than 1,000 views. For GC content in bilsulfite converted library
Popular Question 6 months ago, created a question with more than 1,000 views. For Sort Multiple Fasta Numerically
Popular Question 7 months ago, created a question with more than 1,000 views. For Sort Multiple Fasta Numerically
Commentator 7 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 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 8 months ago, created a question with more than 5,000 views. For Bedtools "Segmentation Fault" While Working With Genome.Fa
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Extract According To Row
Popular Question 11 months ago, created a question with more than 1,000 views. For Pcr Primer In Highly Repetitive Region
Commentator 11 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 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 ?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Extract According To Row
Scholar 13 months ago, created an answer that has been accepted. For A: Bedtools intersect with minimum overlap required as a number
Popular Question 14 months ago, created a question with more than 1,000 views. For Pcr Primer In Highly Repetitive Region
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Extract According To Row
Scholar 14 months ago, created an answer that has been accepted. For A: Bedtools intersect with minimum overlap required as a number
Popular Question 14 months ago, created a question with more than 1,000 views. For Pcr Primer In Highly Repetitive Region
Popular Question 15 months ago, created a question with more than 1,000 views. For Blast2 Like Local Aligner
Popular Question 16 months ago, created a question with more than 1,000 views. For Blast2 Like Local Aligner
Great Question 17 months ago, created a question with more than 5,000 views. For Counting N'S Within Fasta
Popular Question 17 months ago, created a question with more than 1,000 views. For Blast2 Like Local Aligner
Popular Question 18 months ago, created a question with more than 1,000 views. For Blast2 Like Local Aligner
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 ?
Popular Question 18 months ago, created a question with more than 1,000 views. For Blast2 Like Local Aligner
Popular Question 18 months ago, created a question with more than 1,000 views. For 7N Motif Search Over The Genome
Popular Question 18 months ago, created a question with more than 1,000 views. For 7N Motif Search Over The Genome

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