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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
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Basti
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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
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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…
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ATpoint
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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
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scholaraspect2008
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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
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hkarakurt
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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
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Thank you @atpoint for your response. However, aim of analysing to generate a matrix with all dataset available after batch correction.
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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
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rj.rezwan
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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
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ATpoint
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This has been asked so many times before. Analyse them separately, then make a statement on reproducibility of results using a meta-analysi…
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What is qcovhsp (high scoring segment pair) in BLAST output. Can we use this parameter to calculate the gene coverage?
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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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