User: S

gravatar for S
S80
Reputation:
80
Status:
Trusted
Location:
United States
Last seen:
11 hours ago
Joined:
4 years, 6 months ago
Email:
s******@rocketmail.com

Posts by S

<prev • 23 results • page 1 of 3 • next >
0
votes
1
answer
51
views
1
answers
Comment: C: Locally installed RNAfold does not color the predicted secondary structure
... Thanks, Pierre! Do you know of a way to color it using "base-pairing probabilities" just like the structure produced by the RNAfold webserver? ...
written 14 days ago by S80
0
votes
1
answer
51
views
1
answer
Locally installed RNAfold does not color the predicted secondary structure
... Hi Everyone, I downloaded a command line version of the RNAfold package on linux server and I am trying to predict the secondary structure of the RNAs. Everything is working fine except the predicted secondary structure is has no color annotations (it is black and white) unlike the secondary struct ...
rnafold rna secondary strcuture written 14 days ago by S80
0
votes
0
answers
218
views
0
answers
Comment: C: Trimmomatic not trimming the adapter
... Yup. That is the first thing I checked. Thanks for the suggestion though. ...
written 5 weeks ago by S80
0
votes
2
answers
144
views
2
answers
Comment: C: miRNA/smallRNA adapter triming: Any recommendations for adaptor error rate and s
... I work with small RNA data. I think the value of m is very short especially if you are only looking into miRNAs. We typically have a min cutoff of 18 and a maximum cutoff of 34. Otherwise, the q and e values that you used are reasonable. Can you share some references talking about the need for miRNA ...
written 6 weeks ago by S80
0
votes
2
answers
333
views
2
answers
Comment: C: How can I contribute to the Bioinformatics community as a Software Engineer
... Hi Chen, You could contact PIs in different biology research areas that are into developing tools to address biological questions. Even though most of them would require some kind of "commitment" with the tool development time frame but I am pretty sure majority will appreciate your contribution. E ...
written 6 weeks ago by S80
0
votes
0
answers
218
views
0
answers
Comment: C: Trimmomatic not trimming the adapter
... Hi finswimmer, The contents of the adapter.fa is indicated in my question under the double asterisk. I meant for it to be displayed in bold but not sure why it isn't. I think it is because it is under the code block? Below is the raw sequence with the quality values. @SN741:1069:CCAUHACXX:2:22 ...
written 6 weeks ago by S80
1
vote
0
answers
218
views
0
answers
Comment: C: Trimmomatic not trimming the adapter
... Hi Alex, I actually did try a different tool in the meantime. I tried cutadapt and it worked perfectly. However, I am still wondering whether Trimmomatic will still work for this or not. Thanks! ...
written 6 weeks ago by S80
0
votes
1
answer
145
views
1
answers
Comment: C: How to make a gene expression correlation graph?
... Hi Unawaz, There are many ways of representing that but it all depends on the data you have and the information you would like the reader to get. How many genes are we talking about? What is the range of the expression values (or logFC)? For example, Pearson's correlation will generate a value -1 t ...
written 6 weeks ago by S80
0
votes
0
answers
218
views
0
answers
Comment: C: Trimmomatic not trimming the adapter
... Sorry, I will do next time, I overlook it. Thanks! ...
written 6 weeks ago by S80
2
votes
0
answers
218
views
0
answers
Trimmomatic not trimming the adapter
... Hello, I am using Trimmomatic to trim the adapter sequence from the raw small RNA data. For some reason after trimming I still find the adapter in the trimmed sequence. Does anyone have any suggestion? This is the command I am using: java -jar trimmomatic SE -phred33 -threads 10 file_in file_ ...
trimmomatic small rna written 6 weeks ago by S80 • updated 3 days ago by Biostar ♦♦ 20

Latest awards to S

Great Question 3.7 years ago, created a question with more than 5,000 views. For Obtaining the top matches from blast
Popular Question 3.7 years ago, created a question with more than 1,000 views. For blast output using -6 format option
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Obtaining the top matches from blast
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Identifying collinearity between genomes

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1132 users visited in the last hour