User: leo1985.arnab

Reputation:
0
Status:
New User
Last seen:
4 weeks, 1 day ago
Joined:
4 months, 2 weeks ago
Email:
l************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by leo1985.arnab

<prev • 22 results • page 1 of 3 • next >
0
votes
1
answer
147
views
1
answers
Comment: C: Sequence extraction based on coordinates
... Thanks a lot for the solution Alex !! ...
written 4 weeks ago by leo1985.arnab0
3
votes
1
answer
147
views
1
answer
Sequence extraction based on coordinates
... I have a file with sequences in first column and start coordinate for these sequences in the 3rd column. I want to extract all rows where the starting loci of sequences vary by 5 nt of each other. Following is an example Sequence Column header_xxx Start coordinate ...
sequence written 4 weeks ago by leo1985.arnab0 • updated 4 weeks ago by Alex Reynolds19k
0
votes
0
answers
128
views
0
answers
Comment: C: Count of mapped reads
... Okay thanks. Yes, that is what I want. Sorry if that was not clear from my writing. I will try BBMap then. ...
written 5 weeks ago by leo1985.arnab0
0
votes
0
answers
128
views
0
answers
Comment: C: Count of mapped reads
... Oops- apologies for posting incorrectly. Thanks for the suggestion. The sequences in the fasta file are between 22-30 nucleotides in length. I am going to try out featureCounts and see how that goes. Thanks ! ...
written 5 weeks ago by leo1985.arnab0
0
votes
0
answers
128
views
0
answers
Comment: A: Count of mapped reads
... Yes @genomax. you are correct. I want to know for every sequence how many different places it can map to and then report the total number of mapped hits for that sequence. This eventually translates into total number of mapped reads for that sequence. ...
written 5 weeks ago by leo1985.arnab0
0
votes
0
answers
128
views
0
answers
Count of mapped reads
... Hello, I have around 12,000 smallRNA reads (sequences) for which I need to find the total mapped reads for EACH individual sequence. They are in a collapsed fasta file ensuring the sequences appear only once in the entire file (trimming and quiality filtering etc have been already done ). I want to ...
sequence written 5 weeks ago by leo1985.arnab0
0
votes
1
answer
136
views
1
answers
Comment: C: Nucleotide character position in sequence extract
... Wonderful ! Thanks ! That worked out great. Just needed to remove the -m1 at the end as I wanted to search through the whole file. ...
written 6 weeks ago by leo1985.arnab0
2
votes
1
answer
136
views
1
answer
Nucleotide character position in sequence extract
... I have a text file with ~ 60,000 sequences ( 1 sequence per line) I am trying to extract all the sequences that begin with an A (first nucleotide position in the sequence ) and in the ***same sequence*** there should a T at the 10th position. For example: Let's say these are 3 sequences in the 60, ...
sequence written 6 weeks ago by leo1985.arnab0 • updated 6 weeks ago by Pierre Lindenbaum94k
0
votes
1
answer
179
views
1
answers
Comment: C: miRanda target information extraction
... Thanks Pierre ! But I as I have over hundred of entries in the output file (above is a snippet of that file) is there any way I could extract **all** the entries matching **entry #1** from above? Thanks and regards ! ...
written 4 months ago by leo1985.arnab0
0
votes
1
answer
179
views
1
answer
miRanda target information extraction
... Hello, I have the output generated from miRanda. My question is as follows: I want to extract the line ( protein information) **After** the "Read Sequence:" part. I tried grep with -A1 option but that generates information after every single "Read Sequence:" in the **ENTIRE** output file. Bu ...
sequence written 4 months ago by leo1985.arnab0 • updated 4 months ago by Pierre Lindenbaum94k

Latest awards to leo1985.arnab

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1470 users visited in the last hour