Moderator: genomax

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genomax54k
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Posts by genomax

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Comment: C: Parsing large sequence file into per-sample files after barcodes/primers removed
... No worries. Just wanted to make sure what the requirement was since those two require different paths. ...
written 8 hours ago by genomax54k
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Answer: C: Parsing large sequence file into per-sample files after barcodes/primers removed
... 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 genomax54k
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Comment: C: De-replicating sequence file after barcodes/primers removed.
... > 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 genomax54k
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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 genomax54k
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Comment: C: BLAST based on 100k sequences rnaseq?
... > 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 genomax54k
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Comment: C: Batch pairwise alignment and consensus
... 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 genomax54k
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Answer: C: BLAST based on 100k sequences rnaseq?
... 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 genomax54k
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Comment: C: bcftools roh: short way to put several samples from a merged VCF in the same col
... 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 genomax54k
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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 genomax54k
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Comment: C: Boxplot each row in a dataset in R?
... 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 genomax54k

Latest awards to genomax

Scholar 8 hours ago, created an answer that has been accepted. For A: Newbie question about sequencing repeatability/genomic coordinate systems
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Mapping paired-end reads to a draft genome using HISAT2
Scholar 3 days ago, created an answer that has been accepted. For A: Newbie question about sequencing repeatability/genomic coordinate systems
Appreciated 3 days ago, created a post with more than 5 votes. For NovaSeq from Illumina (updated info)
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Mapping paired-end reads to a draft genome using HISAT2
Good Answer 5 days ago, created an answer that was upvoted at least 5 times. For A: Big news from Microsoft. BASH on windows.
Appreciated 5 days ago, created a post with more than 5 votes. For NovaSeq from Illumina (updated info)
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Mapping paired-end reads to a draft genome using HISAT2
Appreciated 8 days ago, created a post with more than 5 votes. For NovaSeq from Illumina (updated info)
Scholar 12 days ago, created an answer that has been accepted. For A: Newbie question about sequencing repeatability/genomic coordinate systems
Commentator 13 days ago, created a comment with at least 3 up-votes. For C: Expression of a gene across all cancer datasets
Scholar 15 days ago, created an answer that has been accepted. For A: Newbie question about sequencing repeatability/genomic coordinate systems
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: What is the difference between GRCh37 and hs37? And hg19?
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: What is the difference between GRCh37 and hs37? And hg19?
Commentator 18 days ago, created a comment with at least 3 up-votes. For C: Expression of a gene across all cancer datasets
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Mapping paired-end reads to a draft genome using HISAT2
Commentator 19 days ago, created a comment with at least 3 up-votes. For C: Removing N's from NextSeq reads
Scholar 19 days ago, created an answer that has been accepted. For A: Newbie question about sequencing repeatability/genomic coordinate systems
Scholar 19 days ago, created an answer that has been accepted. For A: Newbie question about sequencing repeatability/genomic coordinate systems
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: Mapping paired-end reads to a draft genome using HISAT2
Scholar 22 days ago, created an answer that has been accepted. For A: Newbie question about sequencing repeatability/genomic coordinate systems
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: Mapping paired-end reads to a draft genome using HISAT2

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