User: caggtaagtat

gravatar for caggtaagtat
caggtaagtat650
Reputation:
650
Status:
Trusted
Location:
Last seen:
1 day, 19 hours ago
Joined:
1 year, 10 months ago
Email:
j************@web.de

Posts by caggtaagtat

<prev • 183 results • page 1 of 19 • next >
0
votes
1
answer
73
views
1
answers
Comment: C: Should I generate a new Index genome in STAR for 50 base reads instead of 100 ba
... It also states, that the ideal step, however, would be to recalculate. So, since it doesn't take that long, it could be slightly beneficial. But you are right, it seems to make no huge difference. ...
written 2 days ago by caggtaagtat650
0
votes
1
answer
73
views
1
answers
Answer: A: Should I generate a new Index genome in STAR for 50 base reads instead of 100 ba
... As far as I know, it could be beneficial to adjust the parameter you stated accordingly. On the other hand, I also read, that it doesn't completly disrupts your data. Edit: let me cite the STAR manual > In case of reads of varying length, the ideal value is max(ReadLength)-1 . In most case ...
written 2 days ago by caggtaagtat650
0
votes
1
answer
55
views
1
answers
Comment: C: Evolutionary distance from as many organisms as possible to humans
... Thank you very much, that's perfect. Now I only have to somehow convert my newick format into a distance matrix. Are you maybe familiar with that in R for example? ...
written 4 days ago by caggtaagtat650
2
votes
1
answer
55
views
1
answer
Evolutionary distance from as many organisms as possible to humans
... Hi, is there something like a simple database where a lot of species are stated with their evolutionary distance to each other? I found TimeTree, which uses TreeBase among others, but I was unfortunatly not able to extract the data from there. Edit: so for anyone with the same problem, you can eas ...
genome relation evolutionary distance written 4 days ago by caggtaagtat650
0
votes
1
answer
159
views
1
answers
Comment: C: Very low percentage of assigned reads using featureCounts
... And did you check for rRNA contamination like genomax recommended? I, for example, always use sortMeRNA. You can sometimes also see this in a shift to the right of the curve in the GC content distribution plot of your FASTQC output. ...
written 11 days ago by caggtaagtat650
0
votes
1
answer
159
views
1
answers
Comment: C: Very low percentage of assigned reads using featureCounts
... Are your reads trimmed adapter content and base calling quality? ...
written 11 days ago by caggtaagtat650
0
votes
1
answer
159
views
1
answers
Comment: C: Very low percentage of assigned reads using featureCounts
... Are you sure your library is reversed stranded? ...
written 12 days ago by caggtaagtat650
0
votes
2
answers
97
views
2
answers
Answer: A: Running SortMeRNA for bulk RNAseq data
... With `FILEBASE=$(basename "${READ_FW/_1.fq.gz/}")` you define the new variable called `$FILEBASE` as a character string using the file name of the respective `READ_FW` file, but without the ending "_1.fq.gz" and without the whole filepath which originally is in the filename too. The endings file en ...
written 16 days ago by caggtaagtat650
0
votes
0
answers
69
views
0
answers
Genome-guided transcriptome reconstruction
... Hi, I am working with an organsim whose transcriptome is not very well annotated concerning the UTRs. So most annotations in the gtf file reach from start to stop codon. Using RNA-seq data, I would now like to expand the annotations to capture at least some of the UTRs. For that, I found a method ...
rna-seq transcriptome written 29 days ago by caggtaagtat650
0
votes
4
answers
4.6k
views
4
answers
Comment: C: what do the headers of the rMATS output files mean?
... This question was concerning the SE file, which contains information about differences in exon skipping. I only know the columns you named from the ASS file, concerning alternative splice site usage. Per definition, alternative splice site usage either lead to an longer or shorter exon, depending on ...
written 5 weeks ago by caggtaagtat650

Latest awards to caggtaagtat

Appreciated 19 days ago, created a post with more than 5 votes. For A: Question about exon/intron counting in RNA-seq dataset analysis
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Scholar 3 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 4 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Scholar 4 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Popular Question 7 months ago, created a question with more than 1,000 views. For STAR do i need --twopassMode ?
Scholar 9 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?
Centurion 12 months ago, created 100 posts.
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?
Scholar 14 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Supporter 16 months ago, voted at least 25 times.
Appreciated 16 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Appreciated 17 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 566 users visited in the last hour