User: goodez

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goodez160
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Kansas City, MO
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Posts by goodez

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Extract uniquely mapped reads from one species
... Sure I will edit my answer to include some code ...
written 1 day ago by goodez160
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Comment: C: Extract uniquely mapped reads from one species
... It's unclear in the question how they did the alignment. If the chromosome names are unique as I'm suggesting, then it's simple to pull out reads from either organism with `grep`. I suggested using `XS:i` to only take uniquely mapped reads, which I don't see mentioned above. Move my post wherever yo ...
written 1 day ago by goodez160
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Answer: A: Extract uniquely mapped reads from one species
... I did this recently but I aligned with bowtie2. Please note I provide code but you would have to modify it slightly for your case. To create the genome index, I edited the chromosome names in each genome fasta file. So instead of chr1, chr2, chr3... I made it hg_chr1, hg_chr2, hg_chr3. And likewise ...
written 1 day ago by goodez160
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Comment: C: What program do I must to use to design primer for especific samples?
... So is your question more about trying to identify these "most conserved regions" in your BAM file? ...
written 1 day ago by goodez160
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Answer: A: What program do I must to use to design primer for especific samples?
... NCBI's primer-blast is helpful [https://www.ncbi.nlm.nih.gov/tools/primer-blast/][1]. You can mostly just design them yourself and don't need to rely on software. [Here's some general tips][2]. [1]: https://www.ncbi.nlm.nih.gov/tools/primer-blast/ [2]: http://www.premierbiosoft.com/tech_notes/ ...
written 1 day ago by goodez160
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Comment: C: Does differential binding analysis across different ChIP-Seq samples makes sense
... This post is rather old, but I stumbled across it and thought it was an interesting question. You can actually deal with the issue of different IP efficiencies if you use spike-in chromatin from another organism that's somewhat closely related. [This paper][1] describes the method and we're currentl ...
written 1 day ago by goodez160
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Comment: C: Remove extra sequences without unique names from fasta
... If you are executing the code on a single line as you wrote, then remove the `\` characters because those are meant to ignore the new lines as Pierre wrote it. I recommend structuring it just as Pierre did in a text file. Try `nano rm_dup_fasta.sh`, then copy Pierre's code into the file. `chmod ...
written 2 days ago by goodez160
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Comment: C: Remove extra sequences without unique names from fasta
... +1 for linking that very useful GitHub page. Never thought of linearizing a fasta before. Do you know if that awk line works for all fasta files, whether or not there are new lines within the sequences? ...
written 2 days ago by goodez160
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Comment: C: Remove extra sequences without unique names from fasta
... It looks like the awk step essentially converts from standard fasta format into a format of one entry per line. From there it's possible to use sort to only keep unique lines based on the fasta ID. The final step converts it back to normal fasta format (remove tabs, replace with new lines). ...
written 2 days ago by goodez160
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Comment: C: Remove extra sequences without unique names from fasta
... By the way, the reason your `grep | uniq -c` did not work is because you need to sort before piping to uniq. So: ``` grep "^>" file.fa | sort | uniq -c ``` ...
written 2 days ago by goodez160

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Commentator 6 days ago, created a comment with at least 3 up-votes. For C: Single Cell mRNA Seq basic question

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