Moderator: ATpoint

gravatar for ATpoint
ATpoint31k
Reputation:
31,320
Status:
Trusted
Location:
Germany
Last seen:
4 hours ago
Joined:
3 years, 11 months ago
Email:
a*********@gmail.com

PhD Student Genomics (Wetlab/Drylab) {^Enter|fancy|buzzwords$}

Posts by ATpoint

<prev • 4,534 results • page 1 of 454 • next >
0
votes
1
answer
28
views
1
answers
Answer: A: Failed to run Bismark tool on fasta file
... `USAGE: bismark [options] {-1 -2 | } []` You provided no genome folder therefore the control1.fasta is interpreted as the directory that stores the index. ...
written 4 hours ago by ATpoint31k
0
votes
1
answer
743
views
1
answers
Comment: C: GSEA on preranked list with weighted enrichment statistic (exponent=1) in R
... https://www.biostars.org/u/15519/ sorry for hijacking this thread with an unrelated question but I do not think this one here merits a separate thread. What is your opinion on FDR correction? Standard GSEA uses FDR of 0.25 as cutoff as explained in their manual. Can you comment if this is also appro ...
written 5 hours ago by ATpoint31k
0
votes
0
answers
26
views
0
answers
Comment: C: TCR/BCR repertoire Analysis
... Hello phoenix.sum13! We believe that this post does not fit the main topic of this site. This is no bioinformatics-related. Please browse current literature and preprints. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can h ...
written 5 hours ago by ATpoint31k
0
votes
2
answers
42
views
2
answers
Comment: C: How to separate Miseq data and Hiseq data
... ![enter image description here][1] You can upvote and accept more than one answer. [1]: https://image.ibb.co/dfsqrx/upvote_accept_bookmark.png ...
written 5 hours ago by ATpoint31k
0
votes
3
answers
2.7k
views
3
answers
Comment: C: LEADING and TRAILING in TRIMMOMATIC
... Please stop adding this answer to old threads. It does not add to this or the question you posted this to before. This question here has an accepted answer already so no need to refresh it. ...
written 8 hours ago by ATpoint31k
0
votes
0
answers
34
views
0
answers
Comment: C: Compare the variances of multiple categorical distributions in a repeated measur
... Right-click the image on the image hoster website to get the ful link (https://i.imgur.com/Hjt6RBO.png), then paste this into the image field. I made the change for you. ![enter image description here][1] Even though we have some members here with statistics expertise I guess you could get more re ...
written 15 hours ago by ATpoint31k
0
votes
0
answers
36
views
0
answers
Comment: C: Filter out supplementary aligned reads for variant calling or not
... In general it is good practice to not do any custom filtering unless the manual of the tool you use specifically recommends it. You should have duplicates marked in the BAM. Any proper variant caller will then internally choose the reads that based on its underlying model or strategy are suitable. T ...
written 17 hours ago by ATpoint31k
0
votes
0
answers
61
views
0
answers
Comment: C: Exonerate killed automatically
... I would re-run it and monitor memory usage. Probably you ran out of memory. Maybe try with like 10 sequences to see if it is a general problem. ...
written 18 hours ago by ATpoint31k
0
votes
1
answer
60
views
1
answers
Comment: C: MACS for a paired-end sequencing
... Agreed. PE data have to be mapped together otherwise the advantage of the method is gone and you would be double-counting every read. Once you have a paired-end BAM file just use `-f BAMPE` as parameter in macs. It will take care of the rest. ...
written 21 hours ago by ATpoint31k
1
vote
2
answers
146
views
2
answers
Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
... That all sounds reasonable. As said it is difficult to tell from remote. I would stick with the standard workflow including normalization which is well-tested and accepted, so basically running `DESeq()`. ...
written 1 day ago by ATpoint31k

Latest awards to ATpoint

Teacher 1 day ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Appreciated 3 days ago, created a post with more than 5 votes. For C: Detect repeats problematic for PCR
Teacher 6 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 6 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Scholar 6 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 7 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Teacher 7 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 7 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Scholar 8 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Popular Question 9 days ago, created a question with more than 1,000 views. For Tool to identify recurrent mutations directly from VCF
Scholar 12 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 12 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 14 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 15 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Teacher 15 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Popular Question 16 days ago, created a question with more than 1,000 views. For Tool to identify recurrent mutations directly from VCF
Scholar 18 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 19 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?
Scholar 19 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Scholar 20 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Scholar 21 days ago, created an answer that has been accepted. For C: Does BWA mem work with uBAM file?
Teacher 23 days ago, created an answer with at least 3 up-votes. For C: Does BWA mem work with uBAM file?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1048 users visited in the last hour