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Recent Replies
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: DEA Solver Learning Version 8
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GenoMax
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Can you add a note about what this software is used for? Content on this site needs to be related to bioinformatics otherwise it may be rem…
Comment: 4 Fastq files for a single run generated by 10X
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hkarakurt
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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
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Sumeet
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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.
Comment: what should I do if I get a compromised sample of scRNA-seq data?
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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
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aanchal.yadav
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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
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Jeremy
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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…
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
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peanut
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Thank you for your answer,but after verifying the protein file, it seems there is no problem. Even if there are missing codons, the program…
Comment: Finding human .vcf files online to download
by
cmdcolin
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i can't really tell you why your code doesn't work if you dont provide it. and, if you describe as much as possible what your goals are, th…
Answer: Help with gatk CreateSequenceDictionary
by
MatthewP
★
1.3k
maybe try?:
-R /variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa -O /variant_calling/Desktop/demo/supporting_files/hg38/hg3…
Comment: Java error while running HiCDC overview code
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Brian Bushnell
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Looks like you have corrupt or improperly-formatted input. It's expecting to parse a floating-point number where the word "score" appears.…
Comment: what should I do if I get a compromised sample of scRNA-seq data?
by
dsull
★
5.1k
The knee plot is just one type of QC. I'd say just proceed with your analysis and see if you observe anything funky (analysis itself is a Q…
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