User: deep771992chanda

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Posts by deep771992chanda

<prev • 8 results • page 1 of 1 • next >
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LEFSE: Should I remove features with low relative abundance or lefse will take care of it?
... Hi… I have pathway abundance outputs from HUMAnN 3.0. I want to find out differentially abundant pathways between two groups. For that, I have removed those features (pathways) which are not present in at least 10% of the total samples. But, in addition, should I also need to remove those features w ...
lefse written 2 days ago by deep771992chanda10
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What effect size value should I use for differential abundance of microbiome taxa?
... Hi there!!! I am using `ALDEx` for differential abundance analysis of microbiome taxa. In this case what "`effect size`" value between `0 to 1` will you suggest for a perfect (or say good) statistical analysis? I am using P-value as <0.05. Thanks ...
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Comment: C: How to multiply all columns of a .csv table with a constant extracted from anoth
... Sir, I am not familiar with programming. So, I am not sure what do you mean by "I don't know how fixed your output format is". And, regarding point 3 > I'm assuming all your values are 0.00123. If you need to account for integers etc too, then the regex needs to change. , the second column is ...
written 10 days ago by deep771992chanda10
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Comment: C: How to multiply all columns of a .csv table with a constant extracted from anoth
... Yes. It is supposed to be a .csv file only. Actually, I modified so that it can look a table here in the post. It should be like: # Gene Family ERR260136_Abundance-RPKs UNMAPPED 0.445035 UniRef90_A0A015P9C8 0.00080211 UniRef90_A0A015P9C8|g__Bacteroides.s__Bacteroides_fragilis ...
written 10 days ago by deep771992chanda10
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Comment: C: How to multiply all columns of a .csv table with a constant extracted from anoth
... It is not an assignment. I need this operation while analyzing genomic data. Being new in programing I can only find out read counts for a sample from the first file (`read_count.csv`) by this: awk /ERR260136/{'print'} read_count.csv | awk {'print$2'} Can you please show me some way? I am stuc ...
written 11 days ago by deep771992chanda10
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How to multiply all columns of a .csv table with a constant extracted from another table?
... I have 20 files where the filenames are like: `ERR260136.genefamilies.csv`, `ERR276187.genefamilies.csv`, etc. Each file has to be multiplied by one constant. The corresponding constant has to be taken from a `.csv` file named `read_count.csv`. The `read_count.csv` file is like: SampleID Read_c ...
bash written 11 days ago by deep771992chanda10 • updated 9 days ago by davidattenboroughcbd0
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Comment: C: How to extract out specific information from files within a directory?
... Thanks sir. But, to my knowledge it will just print the all lines containing the term "final pair". ...
written 12 days ago by deep771992chanda10
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How to extract out specific information from files within a directory?
... I have a around 50 files which are named in the format: ERR*.log (i.e. ERR23432.log, ERR12356.log, and so on...). From each file I want to extract a specific information (value). Within each file, there are values at the end of the lines: `final pair1 : Total reads after merging results from multi ...
python grep regex written 12 days ago by deep771992chanda10 • updated 12 days ago by zx87549.7k

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