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Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
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Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
mRNA file is not going to have the same co-ordinates as the main chromosomes. Can you clarify what coordinates are in your BED file?
Comment: Downloading a list of all refseq assembly ids, including supressed assembliey
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GenoMax
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Can you provide examples of suppressed ID's?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
It is because I want to pull the mRNA fasta files and not DNA (which I guess is the case if I pull it from the entire genome)
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If your intervals are for main chromosomes why are you using the mRNA file instead of the entire genome? If you have the gene ID's you coul…
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
by
Pierre Lindenbaum
160k
I downsampled the bams and it works now...
Answer: ONT direct RNA sequencing
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dthorbur
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You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
Comment: Nanopore data filtering using fastp
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emilydolivo97
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I tested seqtk sample but I generate a wird result. Can I share my code and results with you please ?
Comment: Nextflow ERROR : Timeout waiting for connection from pool
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GenoMax
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As best as I can tell it is a combination of things. Did you try setting `export NXF_ENABLE_VIRTUAL_THREADS="true"` in your shell? You also…
Comment: Coverage observed in introns in the Knockdown genes but not in knockout genes
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rohitsatyam102
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As per the image below obtained by Running RNASeQC the intronic reds aren't that much (See the knockdown samples enclosed in the Red box) (…
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Joe
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Am I understanding this correctly, that what you are looking for is any sequence where *any part* of the coord range overlaps with *any oth…
Comment: convert cds to seurat object
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edoardofilippi1998
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Did you check the data in the assay of the cell_data_set object?
Comment: calculate mismatch rate from VCF file
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Pierre Lindenbaum
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use the output of `samtools mpileup`
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ATpoint
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It's `-log10(pvalue)`, you miss the minus. Some people use indeed pvalue, but since you're filtering on padj, I would show `-log10(padj)` r…
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
Thank you for your reply!! My bad. I didn't mention that I want to get the mismatch rate for each site. Is this error rate for each site?
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by
dthorbur
★ 1.7k
Parallelize. Chunk your transcriptome into groups of something like 5000 (or less if you want it to go faster), and run an array across you…
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