Moderator: dariober

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dariober9.1k
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Posts by dariober

<prev • 788 results • page 1 of 79 • next >
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Comment: C: Does BWA mem ever edit data
... > running BWA, discarding all but the name, sequence and quality So why don't you archive fastq in the first place? I don't see the reason to align and then discard the work the aligner has done. If you really want to store unaligned CRAM instead of fastq then you can convert fastq to unaligned ...
written 4 days ago by dariober9.1k
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Answer: A: script for task or AWK
... Another option is to use [bedtools groupby](http://bedtools.readthedocs.io/en/latest/content/tools/groupby.html): sort -k1,1 -k2,2n data.txt | groupBy -g 1,2 -c 3,3,3 -o min,max,count seq000001 Fc06 35.948 51.086 72 seq000001 Fc08 37.009 37.916 2 seq000002 Fc06 63.754 63.754 2 ...
written 7 days ago by dariober9.1k
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Answer: A: How to assess the Fold-change significance using a t-test in R?
... Granted that with just one data-point you can't do much without making further assumptions. It seems to me that you want to know how *extreme* your log-fold change is. For this, you could make a guess, more or less driven by data you have, about the distribution of log-fold changes from which your d ...
written 11 days ago by dariober9.1k
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Comment: C: Installing IGV on Bio-linux 8 - Installing All Dependancies At Once
... Hello- See edited answer ...
written 14 days ago by dariober9.1k
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Answer: A: Installing IGV on Bio-linux 8 - Installing All Dependancies At Once
... I don't think you need *install* IGV, you just [download][1] the binary distribution, unzip it and execute `./igv.sh` To make all users (`a`) able to execute (`x`) `igv.sh`: chmod a+x igv.sh Don't worry about the other files. On Linux, you don't start IGV by double-clicking on an icon (or m ...
written 16 days ago by dariober9.1k
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Answer: A: Picard liftoverVCF error when attempting to liftover to build 38
... I've been banging my head on this for the last couple of hours... The fix (for me at least) is to add to `LiftoverVcf` the option `WARN_ON_MISSING_CONTIG=true` My command: java -Xmx6g -jar picard.jar LiftoverVcf I=22.fix.vcf.gz O=22.lo.vcf.gz \ CHAIN=hg19ToHg38.over.chain.gz \ ...
written 19 days ago by dariober9.1k
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Answer: A: What is the computation requirement to process whole genome paired end data each
... Just a rough estimate... You have 340 GB of fastq (170 x 2, I assume this is **uncompressed**). Aligned and in BAM format this may be ~50 GB. To sort it you need another 50 GB for the temporary files and 50 GB for the final aligned BAM. You could pipe the output of the aligner (say `bwa mem`) into ` ...
written 20 days ago by dariober9.1k
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Comment: C: statistics data, observed vs expected values
... Can you post an excerpt of your data.frame? Or all of it if not too big, possibly anonymizing the confidential information in it. ...
written 29 days ago by dariober9.1k
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Answer: A: How can I compute if the co-occurrence of two TFBSs within a certain width in al
... I'm not sure I fully understand your question but maybe [GAT](http://gat.readthedocs.io/en/latest/) and/or [bedtools reldist](http://bedtools.readthedocs.io/en/latest/content/tools/reldist.html) could do the job... ...
written 4 weeks ago by dariober9.1k
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Answer: A: Bimodal p-value distribution
... Not really answering your question just a couple of thoughts... * This article has some comments about the shape of the p-value distribution [inspection-and-correction-of-pvalues](http://www-huber.embl.de/users/klaus/Teaching/DESeq2Predoc2014.html#inspection-and-correction-of-pvalues) in case you h ...
written 6 weeks ago by dariober9.1k

Latest awards to dariober

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 7 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Scholar 23 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 10 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 12 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Scholar 3 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 4 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Appreciated 4 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Popular Question 5 months ago, created a question with more than 1,000 views. For Trim & align paired-end reads in a single pass
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 6 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 6 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Scholar 7 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam

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