User: Nitin Narwade

gravatar for Nitin Narwade
Nitin Narwade310
Reputation:
310
Status:
Trusted
Location:
NCCS, Pune
Last seen:
4 days, 18 hours ago
Joined:
2 years, 1 month ago
Email:
n***************@gmail.com

Posts by Nitin Narwade

<prev • 70 results • page 1 of 7 • next >
0
votes
0
answers
84
views
0
answers
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 9 days ago by Nitin Narwade310
0
votes
3
answers
148
views
3
answers
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 days ago by Nitin Narwade310
0
votes
0
answers
112
views
0
answers
Comment: 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 12 days ago by Nitin Narwade310
0
votes
3
answers
173
views
3
answers
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 12 days ago by Nitin Narwade310
0
votes
3
answers
173
views
3
answers
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 12 days ago by Nitin Narwade310
0
votes
0
answers
107
views
0
answers
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 13 days ago by Nitin Narwade310
1
vote
0
answers
135
views
0
answers
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 13 days ago by Nitin Narwade310
0
votes
0
answers
81
views
0
answers
Comment: C: How to make a plot with gProfileR results?
... In this tutorial, they have used web-based g:Profiler for the enrichment analysis and cytoscope for the representation. It may help you. ...
written 13 days ago by Nitin Narwade310
0
votes
3
answers
135
views
3
answers
Comment: C: How do I replace the values in one file with the values in another file?
... Dear giegie, I have updated the above code, please try with this. You have to run it using (Assuming you have saved this code with name `script.py`) command like `python script.py input1.tsv input2.tsv output.tsv` `output.tsv` file will generate with contents given below. chr1 710000 715000 ...
written 13 days ago by Nitin Narwade310
1
vote
3
answers
135
views
3
answers
Answer: C: How do I replace the values in one file with the values in another file?
... Here is a simple python code, that you can use. **By the way where you are going to use this file. Is it an input for some specific tool or server?** ### ## ## USAGE: python script.py input1.tsv input2.tsv output.tsv ## ### import sys try: file1 = sys.arg ...
written 13 days ago by Nitin Narwade310

Latest awards to Nitin Narwade

Scholar 5 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
Teacher 5 weeks 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1921 users visited in the last hour