Moderator: 5heikki

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5heikki7.2k
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Posts by 5heikki

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Comment: C: BLAST in Linux - SOCK_SetupSSL
... My guess is that your Linux has tblastx in $PATH, however, it's so old that it doesn't support https. You can verify with `tblastx -version` The actual tblastx of blast 2.7.1 should be in ~/Documents/ncbi-blast-2.7.1+/bin/ and thus the call would be `~/Documents/ncbi-blast-2.7.1+/bin/tblastx -db ...
written 18 days ago by 5heikki7.2k
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Answer: A: Judging best assembly
... If there's a closely related genome available, why aren't you doing a reference guided assembly? Also, it might be a good idea to try different assemblers. As to your two assemblies, they're essentially same except the bigger one includes more short contigs that may or may not be "good". I would go ...
written 19 days ago by 5heikki7.2k
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Comment: C: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... But then you might download representative over reference or vice versa randomly (depending how the file is sorted). Of course that might not matter. You could sort the assembly summary file first based on that column. At least then it would be consistent for sure.. ...
written 24 days ago by 5heikki7.2k
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Comment: C: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... In those two cases the first match has "representative genome" in the fifth column. I don't know if NCBI has ordered the file that way. Perhaps it would be wiser to filter for that if "reference genome" fails. Then if you still get empty query you can take the first match or alternatively look into ...
written 24 days ago by 5heikki7.2k
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Answer: A: Retrieve reference genome for a taxonomic id from NCBI automaticaly
... #!/bin/bash TAXID="$1" if [[ -z "$TAXID" ]]; then echo "Usage: retrieveReference.sh NcbiTaxId" exit else if [[ ! -e assembly_summary_genbank.txt ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt fi ...
written 24 days ago by 5heikki7.2k
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Answer: A: 16S rRNA de novo otu picking analysis
... How could you get GG ID's with de novo OTU picking since reference is never used? You're picking OTUs de novo. And yes, you would have to use closed or open reference OTU picking to get the identifiers. Alternatively, I imagine you can somehow assign IDs to your de novo OTUs post OTU picking. ...
written 25 days ago by 5heikki7.2k
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Comment: C: common sequence between multi fasta file
... Check from `blastn -help` output how to add a field to outfmt for sequence similarity and filter also based on that in the `awk` command. In case the "temp" file is still huge, you must have a lot of redundancy in your input. ...
written 4 weeks ago by 5heikki7.2k
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Comment: C: common sequence between multi fasta file
... If the sequences are really short add `-task blastn-short` to the command. Also, is it possible that you don't have any "universal" seqs? ...
written 4 weeks ago by 5heikki7.2k
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Answer: A: common sequence between multi fasta file
... This assumes that 1) blast is installed and that 2) the script is run in the dir where .fasta named files reside #!/bin/bash FILES=($(find . -maxdepth 1 -type f -name "*.fasta")) for((i=0;i<${#FILES[@]}-1;i++)); do blastn -query ${FILES[$i]} -subject ${FILES[$i+1]} -outfmt '6 ...
written 4 weeks ago by 5heikki7.2k
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Comment: C: using parallel program
... If your data is in format: arg1arg2 arg1arg2 You should actually change the tabs to newlines before piping to parallel, e.g. cat fna.ls | tr "\t" "\n" | parallel ... The script was written for data that was in format like below: arg1 arg2 arg1 arg2 ...
written 4 weeks ago by 5heikki7.2k

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