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Recent Replies
Comment: Illumina reads preprocessing best practice for snp calling applications
by
Enrique
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Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
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The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
Comment: Free/open source 23andme-like analysis
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Thank you, I added 'accurate' now ;)
I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
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Guys, just use `samtools sort` which won't get you into trouble with any of that.
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I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
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For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
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it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
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I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
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Noted that 'accurate' wasn't among your criteria ;)
Anyway, most variant callers are free open-source software. However, for ancestry ana…
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> server so I cannot use Blat for this purpose.
blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
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My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`.
It is…
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thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with
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will look into that. Thank you very much
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