User: Nitin Narwade

gravatar for Nitin Narwade
Nitin Narwade340
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340
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Location:
NCCS, Pune
Last seen:
4 days, 21 hours ago
Joined:
2 years, 4 months ago
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n***************@gmail.com

Posts by Nitin Narwade

<prev • 73 results • page 1 of 8 • next >
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Answer: A: Python3: How to split the tuple generated by the .groupby function in pandas
... The output of `.groupby()` function is tuple but the values of such tuple are dataframe, so we have to access their values using keys. I have just tried one solution using the same approach, it might help you. import pandas as pd data = pd.read_csv('input.txt', header = None, delimiter ...
written 7 weeks ago by Nitin Narwade340
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Comment: C: To obtain transcription start site from a dna sequence
... What is the organism your working on....?? ...
written 7 weeks ago by Nitin Narwade340
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Comment: C: Mock Metagenome Gene Content
... I think taxonomic classification will be the best way to find out abundance of an organism in metagenomic samples. You can you have a look on kaiju in this case. ...
written 8 weeks ago by Nitin Narwade340
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Comment: C: How to write Python script locally?
... 1. It's very simple use any text editor like geany, vscode, textpad, gedit(defualt for linux-ubuntu version). Write your code let's say we have to print `hello python` so write `print ('hello python')` and save it with `.py` extension `Ex. script.py` . Then you can run your code in geany directly ...
written 11 weeks ago by Nitin Narwade340
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Comment: C: How to extract unique values between columns in R ?
... Could you please elaborate the expected output, because it is bit confusing. None of the record in output is maintaining the order as input, neither rowise nor columnwise. ...
written 11 weeks ago by Nitin Narwade340
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Answer: C: How can I use biopython to extract each alpha carbon from a PDB file?
... I am sure there must be some other way to directly parse the structure(using `Bio.PDB.PDBParser` object) and get the records of the selected atom using Bio.PDB module. But here I am directly parsing `.pdb` file and selecting the records of interest using the regular expression from Bio.PDB im ...
written 11 weeks ago by Nitin Narwade340
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Comment: C: macs2 conda installation problem
... I think you need to source the .bashrc file after adding those lines or you can simply restart the session(terminal). And one more tip just run which python2 commamd and set the PYTHONPATH variable as mentioned here Thank you. ...
written 11 weeks ago by Nitin Narwade340
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Comment: C: macs2 conda installation problem
... On my linux(ubuntu 16.04) I usually change the defualt python version by adding alias python='python2' this line at the start of .bashrc file present in the home directory. And if I want to use the syatem's python instead of conda, I will change the $PATH variable added by conda from export P ...
written 11 weeks ago by Nitin Narwade340
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Comment: C: cd-hit-est total seq value doesn't match number of sequences being compared?
... have you considered `-s` parameter? cd-hit-est help for `-s` -s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster ...
written 11 weeks ago by Nitin Narwade340
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Comment: C: Extract sequences from the raw reads
... To extract the gene/promoter sequences from you raw reads, you have to map them on some reference. Here reference does not mean genome all the time. You can make your own customized reference database from the interested gene/promoter sequences and then using any sequence alignment tools (I would ...
written 11 weeks ago by Nitin Narwade340

Latest awards to Nitin Narwade

Scholar 9 weeks ago, created an answer that has been accepted. For A: about bioperl script for extracting sequences from a fasta file(get orf output f
Scholar 3 months ago, created an answer that has been accepted. For A: about bioperl script for extracting sequences from a fasta file(get orf output f
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: about bioperl script for extracting sequences from a fasta file(get orf output f

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