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Recent Replies
Comment: Reading AD and other genotype information from the VCF file
by
Pierre Lindenbaum
166k
`bcftools query -f '[%CHROM %POS %REF %ALT %SAMPLE %GT %AD\n]' `
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
colindaven
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This one has the massive computing resources at the EBI behind it, so I wouldn't worry about capacity. Check their stats.
Answer: Cibersortx server down?
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Yes it is down now (though it was working ~ 3-4 hours ago): https://downforeveryoneorjustme.com/cibersortx.stanford.edu?proto=https
Answer: Available signature matrix for deconvoluting my bulk data using CIBERSORTX
by
Sam
•
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Have you checked out [cellxgene][1]? If you filter by organism you might find one that is suitable.
[1]: https://cellxgene.cziscience.c…
Comment: RNAseq requirements: Biological and Technical replicates
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jkim
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Ouch, my mistake. Updated my comment.
Comment: RNAseq requirements: Biological and Technical replicates
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However, one might argue that multiple biological samples (i.e. multiple blood draws) from each patient might be useful. Still, probably no…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
Mensur Dlakic
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> So maybe this approach will help us find interesting and rare pathways — something along those lines.
Still the same answer as before - …
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by
yuntan1992
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or add parameter "--soft-clipped-unmapped-tlen"
Comment: CIBERSORTx error: 'x' must be an array of at least two dimensions
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ATpoint
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I would take this opportunity to encourage using different tools. Cibersortx is not open, its source code has never been published. That ha…
Answer: CIBERSORTx error: 'x' must be an array of at least two dimensions
by
catarinaventura_pt
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For those still looking for the answer about this, I just figured out that you need to have replicates for it to work.
Comment: CIBERSORTx error: 'x' must be an array of at least two dimensions
by
catarinaventura_pt
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I´m having the same problem here described. Any updates on how to solve this?
Answer: ATAC-seq fragment size distribution - huge spike at 150 bp
by
yuntan1992
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After removing adapters with trim_galore, change the parameter of bowtie2 " --local" to "--end-to-end".
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
shevch2009
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That is a great comparison! :) It definitely looks that way. :)
It's not about taxonomy, but about reconstructing metabolic pathways direc…
Comment: How to connect the UCSC when i get the DMR.plot?
by
Wren
•
0
I tried using the main site but it still didn't work. Thanks anyway, I'll try other methods.
Answer: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
Mensur Dlakic
★
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If you want an overall taxonomic profile, this tool will do it from reads directly:
https://github.com/DessimozLab/read2tree
> Well, …
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