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Recent Replies
Comment: How many reads for WGS Sequencing?
by
Ruqaiya
•
0
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…
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.3k
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?
by
Ruqaiya
•
0
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
•
0
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
by
Francesco
▴
10
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?
by
Francesco
▴
10
Hi! Whenever you do make independent analysis or aggregate data and analyze them, most cell type assignment tools start from raw counts to …
Answer: ChIP-seq datasets: input samples omitted?
by
ATpoint
82k
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
by
ATpoint
82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome
by
gaoanwei
•
0
I found the question and ASK the GPT4 turbo
Answer: Differential Expression using Isoseq-supplemented reference transcriptome
by
gaoanwei
•
0
Your approach seems reasonable and well-informed, though it's perhaps less customary in the field, which could be why you haven't found pap…
Answer: How many reads for WGS Sequencing?
by
Mensur Dlakic
★
27k
It takes 29 seconds to assemble this genome (20 CPUs) with the following statistics:
135 contigs, total 2821177 bp, min 200 bp, max …
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴
530
IMO (and unfortunately) there needs to be an effort to develop these algorithms.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
the samples that are `./.` have no coverage (or not enough to call a genotype) and the `0/0` are homozygous reference
Answer: How many reads for WGS Sequencing?
by
GenoMax
141k
Did you download the complete dataset available from ENA/NCBI SRA? This is an older dataset (from 2012) with a total of 1146212 reads and 1…
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