Moderator: dariober
dariober ♦ 9.1k
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Posts by dariober
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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
dariober ♦ 9.1k
3
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4
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151
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4
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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
dariober ♦ 9.1k
2
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1
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151
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... 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
dariober ♦ 9.1k
0
votes
2
answers
178
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2
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... Hello- See edited answer ...
written 14 days ago by
dariober ♦ 9.1k
0
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2
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178
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2
answers
... 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
dariober ♦ 9.1k
0
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2
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338
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2
answers
... 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
dariober ♦ 9.1k
0
votes
3
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123
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3
answers
... 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
dariober ♦ 9.1k
0
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0
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179
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0
answers
... 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
dariober ♦ 9.1k
1
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129
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... 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
dariober ♦ 9.1k
1
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207
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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
dariober ♦ 9.1k
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