Moderator: genomax
genomax ♦ 54k
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Posts by genomax
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... No worries. Just wanted to make sure what the requirement was since those two require different paths. ...
written 8 hours ago by
genomax ♦ 54k
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... That does look like the original illumina barcode.
It appears that this dataset is from an intermediate step in `qiime` pipeline. Is that correct? `qiime` already has a script available to do this. [See here][1].
[1]: http://qiime.org/scripts/split_sequence_file_on_sample_ids.html ...
written 8 hours ago by
genomax ♦ 54k
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... > I would like to separate this file into per-sample sequence files
that does not jive with the title of this post.
> De-replicating sequence file after barcodes/primers removed.
So do you want to de-duplicate the sequences or separate them into files based on a per sample basis? Depending ...
written 9 hours ago by
genomax ♦ 54k
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Comment:
C: Google search for gene variants
... This post is lacking in detail (you are a moderator so you should be setting a good example). What is the link going to? What do you mean by this?
> alternate ways we fellow researchers search for variants ...
written 9 hours ago by
genomax ♦ 54k
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... > I have received rna-seq data and I want to know what organism it is
> from, that is the assignment.
That specific task is a simple blast search with 10 reads at most (unless you have been given a deliberately contaminated sample). ...
written 9 hours ago by
genomax ♦ 54k
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... If they are going to align like that then what you are looking to do is to merge them into a longer representation, correct? I recommend `bbmerge` from [BBMap suite][1].
[1]: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmerge-guide/ ...
written 12 hours ago by
genomax ♦ 54k
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... Are you only looking to see if there any contamination or are you interested in "everything that is in there and I expect lots of different things" scenario?
For 100K sequences you need to run blast locally. Instead of blast using [DIAMOND][2] against NCBI `nr` collection would be one option. This ...
written 12 hours ago by
genomax ♦ 54k
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... Please use `ADD COMMENT/ADD REPLY` when responding to existing posts to keep threads logically organized.
If you are posting this from China and are not able to use the `ADD COMMENT/ADD REPLY` buttons (ones with gray background highlight) then switch to chrome browser. People have said that works i ...
written 14 hours ago by
genomax ♦ 54k
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Comment:
C: samtools error #E27
...
Hello michael!
Questions similar to yours can already be found at:
samtools error #E27
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!
...
written 1 day ago by
genomax ♦ 54k
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... https://www.biostars.org/u/35172/ : If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
![Upvote|Bookmark|Accept][1]
[1]: http://i68.tinypic.com/2m2ykjr.png ...
written 1 day ago by
genomax ♦ 54k
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For A: Newbie question about sequencing repeatability/genomic coordinate systems
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For A: Mapping paired-end reads to a draft genome using HISAT2
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For C: Trimmomatic: Higher number of "forward only" than "reverse only" surviving reads
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For A: Big news from Microsoft. BASH on windows.
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