User: dariober

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dariober7.7k
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Posts by dariober

<prev • 658 results • page 1 of 66 • next >
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Answer: A: Differences between ensembl gtf files and gff3 file
... Correct me if I'm wrong but it may not be straightforward to apply htseq-count to gff3 (I don't know about featureCount). For typical differential gene expression, htseq-count needs an attribute that groups all the exons belonging to the same gene, the gene_id is usually the right one for gtf. But I ...
written 1 day ago by dariober7.7k
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Answer: A: How to extract reads with no INDEL?
... Isn't it enough to keep reads without I or D operator in the cigar? For this you can use awk like: samtools view -h in.bam chr1:12340-200000 \ | awk '$1 ~ "^@" || $6 !~ "I|D"' \ | samtools view -b - > out.bam ...
written 8 days ago by dariober7.7k
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Answer: A: What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
... Well, since this old thread has been revived I cannot help promoting my own tool. [ASCIIGenome][1] is a genome browser based on command line interface and designed for console terminals. [1]: http://asciigenome.readthedocs.io/en/latest/description.html ...
written 9 days ago by dariober7.7k
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Comment: C: Extracting tlen From BAM File Using htsjdk
... Are you sure the interval chr3:179198825-179199177 contains some reads? Make sure also that "chr3" is correct, maybe your chromosome is named "3". What is the output of `samtools view in.bam chr3:179198825-179199177`? ...
written 10 days ago by dariober7.7k
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Comment: C: Setting up a lab wiki
... Interesting. I've been using GitHub for code and its markdown pages for documentation, similar to Ram's answer I guess. GitLab seems really interesting, do you have any particular reason to prefer it over GitHub? About iRODS, I think/thought this was a pretty heavy weight solution, requiring a dedic ...
written 14 days ago by dariober7.7k
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Comment: C: Collaboration on an empirical QC tool
... +1 from me. One thing I like of FastQC is that it works with minimal input, just give it a fastq file and that's it. This comes at cost of simplistic output of course. Still I think it's important for a QC tool to require minimal configuration, or at least have default settings where all you need is ...
written 14 days ago by dariober7.7k
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Answer: A: Good practices while dealing with very large datasets
... Sort of dodging the issue... Does your question really need hundreds of millions of records to be answered? If not, then you could consider downsampling the data and work with a smaller, random dataset that you can comfortably handle in R. If your analysis involves fitting a linear regression or ot ...
written 21 days ago by dariober7.7k
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Answer: A: htsjdk insert informations from "concordantly mapped" read pairs
... Watch out you have `"Mate End: "` but the code says `rec.getMateAlignment*Start*()` shouldn't it be `rec.getMateAlignmentEnd()`? Maybe try also to look at some read pairs in a genome browser to see where these numbers come from. ...
written 4 weeks ago by dariober7.7k
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Comment: C: How To Efficiently Sort A Fastq File By Entry Id?
... Hi- If you want `xxxx.10` to come after `xxxx.2`, use the `--V/--version-sort` option in the sort command. ...
written 5 weeks ago by dariober7.7k
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Comment: C: why dont we need technical replicate in case of RNA Seq.?
... I would like to link my answer to https://www.biostars.org/p/149538/ about the distinction (or lack thereof) between what are "technical" and "biological" replicates. ...
written 5 weeks ago by dariober7.7k

Latest awards to dariober

Scholar 8 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Good Answer 21 days ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Java Samtools Api: Write Bam To Stdout
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 9 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Popular Question 3 months ago, created a question with more than 1,000 views. For Picard API: Modify sam header
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 4 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Good Question 4 months ago, asked a question that was upvoted at least 5 times. For When and why is bwa aln better then bwa mem?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Appreciated 4 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 5 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 5 months ago, created a post with more than 5 votes. For A: Output the color code according to number
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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets

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