User: gb

gravatar for gb
gb790
Reputation:
790
Status:
Trusted
Location:
Last seen:
1 day, 19 hours ago
Joined:
1 year, 9 months ago
Email:
m**************@gmail.com

Posts by gb

<prev • 162 results • page 1 of 17 • next >
0
votes
1
answer
129
views
1
answers
Comment: C: Can't pair-end fastqs after filtering
... I know you are not comparing R1 and R2. You are comparing two R1 files with each other of the two extractions at least that is what I understand. The primers, mostly called index adapters to demultiplex are different then the primers used for amplification. But now I realise that in your project tho ...
written 1 day ago by gb790
0
votes
1
answer
129
views
1
answers
Comment: C: Can't pair-end fastqs after filtering
... Yes I did, and now again. Clearly I missed something but don't know what sorry ...
written 1 day ago by gb790
1
vote
1
answer
129
views
1
answers
Answer: A: Can't pair-end fastqs after filtering
... I think your approach is wrong. First, the answer to your question is that when you want to merge or assemble paired end reads the R1 and R2 need to be equal. A first quick check would be to check the amount of reads, R1 and R2 need to have the same amount of reads. But if I understand you right and ...
written 2 days ago by gb790
0
votes
0
answers
76
views
0
answers
Comment: C: Not-Merged Reads What to do?
... Do you expect it to merge? I dont think merging is needed if you do an assembly: https://www.biostars.org/p/124298/ ...
written 6 days ago by gb790
1
vote
1
answer
82
views
1
answers
Answer: C: IndexError: list index out of range
... You see the last line? "Fu and Li's test" This line does not contain the ":" character. Open the file and look for this line. You can either manually remove it or add an `if else` or `try except` to your code. ...
written 26 days ago by gb790
1
vote
1
answer
82
views
1
answers
Comment: C: IndexError: list index out of range
... yes, so that means that in one file the structure is slightly different. To know where that difference is you need to print the line before the error. The error is caused by this line: dic[line.strip().split(":")[0]] = line.strip().split(":")[1].strip() And this is because the index is out of ...
written 26 days ago by gb790
2
votes
1
answer
82
views
1
answers
Comment: C: IndexError: list index out of range
... Just debug.... if atrib == aux: print(line) dic[line.strip().split(":")[0]] = line.strip().split(":")[1].strip() You print the line and you check how many ":" characters you see ...
written 26 days ago by gb790
1
vote
1
answer
118
views
1
answers
Comment: C: Binned input for Megan
... I think we need more info. I assume that you want to know which species are present in your sample. Maybe using metaphlan can help http://huttenhower.sph.harvard.edu/metaphlan2. Also think about the classifying part, just blasting all the reads and classifying them is a bit useless due to things lik ...
written 4 weeks ago by gb790
0
votes
1
answer
134
views
1
answers
Answer: A: How to do alpha and beta diversity with shougun metagenome data
... https://www.drive5.com/usearch/manual/cmd_alpha_div.html https://www.drive5.com/usearch/manual/cmd_beta_div.html ...
written 4 weeks ago by gb790
2
votes
1
answer
217
views
1
answers
Comment: C: Why can't import Biopython module when I run my scripts located in /usr/lib/cgi-
... Good that you solved it, but I want to add that you could install anaconda in the /opt folder. This folder is made for this kind of things. http://www.tldp.org/LDP/Linux-Filesystem-Hierarchy/html/opt.html https://sourcedigit.com/22484-linux-opt-directory-open-opt-directory/ http://www.extradrm.co ...
written 5 weeks ago by gb790

Latest awards to gb

Scholar 8 weeks ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Popular Question 3 months ago, created a question with more than 1,000 views. For how to makeblastdb with taxon id's
Scholar 4 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Scholar 6 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Centurion 6 months ago, created 100 posts.
Appreciated 8 months ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: How much I must feel useless?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 10 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Appreciated 11 months ago, created a post with more than 5 votes. For A: Removing Duplicates before aligning
Scholar 11 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Removing Duplicates before aligning
Scholar 16 months ago, created an answer that has been accepted. For A: Clustering of metabarcoding reads from many environmental samples

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 941 users visited in the last hour