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How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
Answer: How to create a mutation frequency comparison plot?
Comment: Best method for batch correction of three datasets
Answer: Calculate GC content for entire chromosome
How Much Coverage Do We Need For An Rna-Seq Experiment?
Answer: Calculate GC content for entire chromosome
Comment: error when installing gistic2 using conda
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Comment: How to interpret the discrepancy of assignment rate in featurecounts using forwa
by
charles.feigin
• 0
I'm having this exact same problem. PolyA RNA-Seq library, running with --fr in hisat2 gives a high fraction of concordant single-mappers, …
Comment: How to create a mutation frequency comparison plot?
by
saipra003
▴ 10
That's awesome thank you. Found out after a bit of researching that this is called a `Cleveland Dot Plot` if anyone else comes across this.
Comment: Cell ranger multi for demultiplexing FB files and GEX files
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GenoMax
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Demultiplexing is typically done using Illumina software? Have you done this already?: https://www.10xgenomics.com/support/software/cell-ra…
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GenoMax
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If you simply want to merge "technical" sequencing replicates then you can do the following cat file1_R1.fastq file1_R1.fastq > merged…
Comment: Best method for batch correction of three datasets
by
CTLong
▴ 20
Thanks for the very descriptive reply. I will give it a try nonetheless because this is pretty much the only way to account for the biologi…
Comment: Installing and importing viennaRNA to python in windows
by
Yun
• 0
Just delete "subprocess.", use p = Popen('RNAfold.exe', stdin=PIPE, stdout=PIPE) instead.
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
by
peanut
• 0
"Okay.Thank you very much."
Comment: Genome coverage of MAGs while submitting to NCBI
by
wn835166087
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Hi, I have a follow up question about this. During my binning process, I obtained the coverage of each contig. Can I take the average cover…
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LauferVA
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Other relevant posts are gathered here. I'll start sorting through these and redact an answer in a day or two if no more specific answer em…
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by
Elise
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Single-nucleus as a part of the 10x multiomics protocol, yes.
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seidel
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> By gaps, I think I mean just sections of the genome where there was not sufficient coverage or data to produce reliable reads for the BAM…
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Please verify your internet connectivity using, say, `ping www.google.com`.
Answer: Calculate GC content for entire chromosome
by
ATpoint
78k
https://www.biostars.org/p/358684/#358687
Comment: error when installing gistic2 using conda
by
luckyday1661
• 0
Sure, creating a new environment still does not work, guess the compatibility still needs to be solved, which is most likely not possible b…
Comment: Building reference dbSNP file using WGS samples
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Brian Bushnell
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I've never seen that before so I'm not quite sure how to replicate it. At a minimum, could you give the exact command you used to generate…
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