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Recent Replies
Comment: How to assign cell types after integration in scRNA
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ATpoint
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https://bioconductor.org/books/release/OSCA.multisample/using-corrected-values.html
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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…
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> What does clipped Fastq mean?
Probably means that NCBI has already scanned and trimmed adapter sequencers.
> both forward and revers…
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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…
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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…
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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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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,…
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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…
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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…
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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…
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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…
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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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