Moderator: ATpoint
ATpoint ♦ 31k
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PhD Student Genomics (Wetlab/Drylab) {^Enter|fancy|buzzwords$}
Posts by ATpoint
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... `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
ATpoint ♦ 31k
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... 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
ATpoint ♦ 31k
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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
ATpoint ♦ 31k
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... ![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
ATpoint ♦ 31k
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... 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
ATpoint ♦ 31k
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... 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
ATpoint ♦ 31k
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... 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
ATpoint ♦ 31k
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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
ATpoint ♦ 31k
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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
ATpoint ♦ 31k
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... 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
ATpoint ♦ 31k
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