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Recent Replies
Comment: How to assign cell types after integration in scRNA
by
ATpoint
82k
https://bioconductor.org/books/release/OSCA.multisample/using-corrected-values.html
Comment: Downloading full alignments from Pfam
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GenoMax
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Not as convenient but the entire set of full alignments can be downloaded here: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pf…
Comment: How many reads for WGS Sequencing?
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> What does clipped Fastq mean?
Probably means that NCBI has already scanned and trimmed adapter sequencers.
> both forward and revers…
Comment: How many reads for WGS Sequencing?
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You can use the default `adapters.fa` file included in the `resources` folder of [**BBMap suite**][1] (program to use is `bbduk.sh`) or a p…
Comment: How many reads for WGS Sequencing?
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Only way to find out is to try. It may work but if it is not going to then you will find that out quick (process would likely crash because…
Comment: How many reads for WGS Sequencing?
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Ruqaiya
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Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing?
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Ruqaiya
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Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
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While I think this is an interesting case, I've before found cleaned 'raw' data on SRA. It happens: bioinformaticians receive the raw data,…
Comment: How many reads for WGS Sequencing?
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Ruqaiya
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1. What does clipped Fastq mean? both forward and reverse reads in the same file?
2. Why would you remove 2000bp contigs? I feel it will gi…
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
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Well, I downloaded both the reads from-[LINK][1]. Thats all i did. Thats the only thing i need to do, right?
I'l try spades.
[1]: http…
Comment: How to assign cell types after integration in scRNA
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Francesco
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Thanks for the fast reply.. however i had only partially understood the answer. Is correct saying that low-representation integration and b…
Answer: Can I run cellassign on samples independently if there is batch effect present?
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Hi! Whenever you do make independent analysis or aggregate data and analyze them, most cell type assignment tools start from raw counts to …
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In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA
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No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
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