User: joe

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joe180
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Posts by joe

<prev • 58 results • page 1 of 6 • next >
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Comment: C: system commands from R containing single and double quotes
... Thanks! I'l try to implement the same with rsamtools/R ...but, I'm still really curious how to solve my initial problem ...
written 23 days ago by joe180
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system commands from R containing single and double quotes
... Hi all, I have a system command which works fine from terminal; samtools mpileup -r chr1:1-100 -B -Q 0 input.sort.bam | awk '{gsub("[^^]","",$5);print length($5)}' > ./output.txt I would like to implement this from R, but can't figure out how to work around the requirement to have both sing ...
R bash written 23 days ago by joe180
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Answer: A: PDB glossary for three letter codes
... In case someone comes back to this, below is something in R that works; system("wget https://ligand-expo.rcsb.org/dictionaries/Components-pub.cif") cif.ref.path <- paste0(getwd(), "/Components-pub.cif") cif.ref.data <- readLines(cif.ref.path) data.grep < ...
written 4 weeks ago by joe180
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PDB glossary for three letter codes
... Can someone point me to a glossary of all three letter codes one might encounter in a .cif file for RNA and DNA? There are some standard ones, as outlined in [the cif dictionary][1] but there are many more I can find... [1]: https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic ...
pdb cif bio3d rpdb R written 4 weeks ago by joe180
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Comment: C: Human snoRNA atlas from small RNA sequencing data in deepBase
... Thanks GenoMax, are you a bot/AI or just omnipresent? (which is almost the same) ...
written 5 weeks ago by joe180
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Comment: C: Human snoRNA atlas from small RNA sequencing data in deepBase
... Hey SnoSeekerNGS devs - in case you're still around, is there any chance this package is still maintained? The binary files that are on the website are not very usable (for linux at least). Any chance you have a compilable version? Thanks!!! ...
written 5 weeks ago by joe180
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Comment: C: NCBI SRA AWS AMI
... This is a great outcome! https://www.amazon.science/latest-news/aws-democratizes-access-to-the-largest-genomic-sequences-repository-nihs-sequence-read-archive ...
written 6 weeks ago by joe180
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Comment: C: genes not mapping to ENTREZID
... So "BLASTing" a sequence will help to identify the source (organism, engineered, etc) and comes in 2 main varieties - by DNA sequence and by protein sequence. BLAST will return a list of proteins/DNA with similarity to your sequence. [https://blast.ncbi.nlm.nih.gov/Blast.cgi][1] Alternatively/addit ...
written 6 weeks ago by joe180
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Comment: C: genes not mapping to ENTREZID
... How did you come up with your gene list? Do you expect the genes to be coding/novel? Try BLASTing the sequences that aren't found, or if you only care about KEGG annotations, you can enter a (protein) sequence in Pfam and look at the domain annotations which you can then relate to a KEGG pathway. ...
written 6 weeks ago by joe180
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Comment: C: UCSC MySQL access
... Turns out my network updated some security stuff which blocked access, so the problem was identified!!! ...
written 10 weeks ago by joe180

Latest awards to joe

Scholar 4 weeks ago, created an answer that has been accepted. For A: mclapply on AWS
Popular Question 4 months ago, created a question with more than 1,000 views. For NCBI SRA AWS AMI
Popular Question 6 months ago, created a question with more than 1,000 views. For NCBI SRA AWS AMI
Popular Question 11 months ago, created a question with more than 1,000 views. For NCBI SRA AWS AMI
Student 15 months ago, asked a question with at least 3 up-votes. For NCBI SRA AWS AMI
Supporter 16 months ago, voted at least 25 times.
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: mclapply on AWS
Scholar 17 months ago, created an answer that has been accepted. For A: mclapply on AWS
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: mclapply on AWS
Scholar 19 months ago, created an answer that has been accepted. For A: mclapply on AWS

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