Moderator: ATpoint

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ATpoint36k
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Germany
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Posts by ATpoint

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Comment: C: bash script for catenating many paired end files
... When you say `catenate` do you mean you want to combine all forwards and all reverse reads into a single forward and a single reverse file, or do you want to combine R1 and R2 for each sample to get an interleaved fastq? Please try something, show the code, we will be happy to debug and guide you. ...
written 4 days ago by ATpoint36k
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Comment: C: Fastq-dump timeout exhausted error
... See https://www.biostars.org/p/366721/ and https://www.biostars.org/p/325010/ These links explain how to directly download fastq files rather than using `fastq-dump` which is sometimes quite unreliable. Version 2.8.0 is very old, consider updating it. ...
written 4 days ago by ATpoint36k
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Comment: C: What are the loci of N on chromosome 21 in hg38?
... Hello prappo13! Questions similar to yours can already be found at: Extracting N positions from fasta file We have closed your question to allow us to keep similar content in the same thread. If you disagree with this please tell us why in a reply below. We'll be happy to talk ...
written 4 days ago by ATpoint36k
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Comment: C: Are Illumina HiSeq 20500 and Illumina NovaSeq 6000 comparable?
... The batch effect between sequencing machines is typically minimal. The more important question is whether this is the only confounding factor. Have the samples been processed identically towards RNA extraction and library prep as well as on the same day? There must be a reason the samples have been ...
written 5 days ago by ATpoint36k
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Comment: C: Python code: too slow to compare two dicts
... It is unfortunate to only show a block of code. Please illustrate the problem by showing input and expected outputs. The answer is probably anyway "use `bedtools intersect`". ...
written 5 days ago by ATpoint36k
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Comment: C: Extract only FASTA headers (+order) from FASTA file
... Solved by OP For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll be happy to talk about it. Cheers! ...
written 6 days ago by ATpoint36k
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Comment: C: Batch correction using DESeq2
... Please consider accepting the answer if it helped solving the issue. ...
written 6 days ago by ATpoint36k
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Comment: C: In search of Mouse limb cell type markers database
... What kind of markers do you need? It differs if you need markers for in silico analysis which would then simply be a set of genes that in its union defines a cluster or if you want to really FACS-out these cells, in which case in would need to be genes expressed as proteins on the cell surface. ...
written 6 days ago by ATpoint36k
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Answer: A: What does minoverlap = 1L means?
... The L notation explicitely makes integers: > class(1000) [1] "numeric" > class(1000L) [1] "integer" Apparently this can have advantages for speed and memory, but this you probably only notice if you work with super large datasets, see https://stackoverflow.com/questions/7014 ...
written 6 days ago by ATpoint36k
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Answer: A: Cannot find faToTwoBit download
... http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ ...
written 6 days ago by ATpoint36k

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