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Jeremy Leipzig
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Recent Replies
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?
by
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
by
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
by
RCMC
•
0
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?
by
Pierre Lindenbaum
158k
how about using the bed file of your targets....
Answer: LCA from BLAST output
by
Dunois
★
2.4k
You should probably be using `MMseqs2`'s `taxonomy` module for this: [https://github.com/soedinglab/MMseqs2#taxonomy][1] .
[1]: https:/…
Comment: autodock vina on mac
by
iamsmor
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0
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?
by
Manuel Sokolov Ravasqueira
▴
100
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…
Comment: WGCNA Dendrogram Branch missing from modules
by
andres.firrincieli
3.5k
I am not familiar with hdWGCNA but perhaps some modules are excluded because their genes are not expressed in a certain proportion of cells.
Comment: LCA from BLAST output
by
Michael
53k
If you know the lineage information is complete you could compare which columns are identical, however, there may be unranked levels in bet…
Comment: Is GeSeq currently unavailable?
by
GenoMax
136k
Email the developers listed on contact page: https://chlorobox.mpimp-golm.mpg.de/contact.html
Comment: Alternative to Gentrome?
by
GenoMax
136k
Curious as to what is `gentrome`? Genome decoy + transcriptome?
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