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Recent Replies
Answer: Best method for batch correction of three datasets
by
ATpoint
78k
Datasets 1 and 2 have nothing in common to serve as batch correction "anchor" (literally speaking), so you cannot correct for anything here…
Answer: contrast file in DESeq2 bioconductor
by
ATpoint
78k
What do you want to compare?
1) You can compare pairwise, like TS vs EOT and TS vs FU and EOT vs FU.
That would be
```r
results(dds, c…
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
by
dthorbur
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890
Ah, there is nothing in your post to suggest you are looking for a specific parameter to ignore a specific warning. I would suggest you edi…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
GenoMax
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You can use
./datasets download genome accession --inputfile file_name_w_accession
`file_name_w_accession` should contain one access…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
here https://stackoverflow.com/a/1521498 is an example how to use read and for loop, you just need to put in your command.
Answer: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
datasets download genome accession --inputfile accessions.txt --include gff3,gbff,rna,cds,protein,genome,seq-report
----------
Or you…
Comment: GEO dataset Microarray data analysis help
by
Basti
★
1.9k
First I advise you to take time to correctly edit your post so that your code is readable. Secondly, you provide a lot of irrelevant code l…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
scholaraspect2008
•
0
hi there, thanks for the reply, is it possible to disclose an example of ./datasets script for that? thank you very much. i m currently try…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
> you can use the commands of curl , wget and slow5curl to download the data from database.
Not in this situation, it is much easier to us…
Comment: Microarray batch correction method suggestions
by
ATpoint
78k
Makes no sense in my opinion. It's different experiments that cannot be quantitatively compared.
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
scholaraspect2008
•
0
by means of that, how should i write my scripting?
say i have
GCF000001
GCF000002
GCF000003
btw sorry if i wasn't that clear with the …
Comment: 4 Fastq files for a single run generated by 10X
by
hkarakurt
▴
180
Thank you for your detailed answer. I will check the reads and compare them with chemistry manual as you suggested.
Thank you again for yo…
Comment: Microarray batch correction method suggestions
by
Sumeet
•
0
Thank you @atpoint for your response. However, aim of analysing to generate a matrix with all dataset available after batch correction.
Comment: what should I do if I get a compromised sample of scRNA-seq data?
by
ATpoint
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Agreed. I would just force the cells to 5000 or so, and then proceed with the normal QC. If there's a lot of trash "cells" in the dataset t…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
rj.rezwan
•
0
you should use the `wild cards` to download all the given above GCF files. Moverover, you can use the commands of `curl` , `wget` and `slow…
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