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Comment: GATK GetPileupSummaries Java heap space
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Comment: which statistical test and which package for comapre datasets?
by
Jeremy
▴ 860
I think you will need at least three replicates to be able to do statistics.
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> Asking for bed file is not a suitable option in the current scenario. ???????
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Manuel Sokolov Ravasqueira
▴ 100
they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> kit is proprietary I can't imagine you get a targeted sequencing without having a BED file....
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
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Manuel Sokolov Ravasqueira
▴ 100
thanks for the suggestion. how can i obtain the bedfile of my targets (kit is proprietary - can I obtain bed from fasta? if yes how?)
Comment: Is interleaved Fastq files the same as interlaced fastq
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rpolicastro
12k
This may indicate that your R1 and R2 reads were processed in a way that didn't maintain the 1:1 order of matching forward and reverse read…
Comment: Is interleaved Fastq files the same as interlaced fastq
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RCMC
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Sorry I accidentally hit enter BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to com…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
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Pierre Lindenbaum
158k
how about using the bed file of your targets....
Answer: LCA from BLAST output
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Dunois
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You should probably be using `MMseqs2`'s `taxonomy` module for this: [https://github.com/soedinglab/MMseqs2#taxonomy][1] . [1]: https:/…
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iamsmor
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thank you but ı am already follow this tutorial steps but at mgltools steps at the page but ı dont undertsand there isnot no enough explana…
Comment: How to create interval list from reference fasta or dict file?
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Manuel Sokolov Ravasqueira
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Hello @MatthewP , were you able to that for a fasta file for example? If you have a fasta file containing a targeted region, how to you ge…
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I am not familiar with hdWGCNA but perhaps some modules are excluded because their genes are not expressed in a certain proportion of cells.
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If you know the lineage information is complete you could compare which columns are identical, however, there may be unranked levels in bet…
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Email the developers listed on contact page: https://chlorobox.mpimp-golm.mpg.de/contact.html
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Curious as to what is `gentrome`? Genome decoy + transcriptome?
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