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Recent Replies
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
GenoMax
136k
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
You need to look into bash scripting regarding reading from a file and using the input in a for loop.
How to combine these is explained her…
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
78k
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…
Comment: Microarray batch correction method suggestions
by
ATpoint
78k
This has been asked so many times before. Analyse them separately, then make a statement on reproducibility of results using a meta-analysi…
Comment: Microbial gene coverage from blast result
by
aanchal.yadav
•
0
What is qcovhsp (high scoring segment pair) in BLAST output. Can we use this parameter to calculate the gene coverage?
Answer: Best way to normalize transcript reads data for PCA & correlation and further bi
by
Jeremy
▴
860
Scaling the data will give you Z-scores. This is a standard way of preparing data for PCA. I would also suggest trying a center-log-ratio…
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