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Admin: genomax

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genomax ♦ 78k
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Posts by genomax

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Comment: C: BiomaRt Many to Many Relationship filtering
... Have you looked at NCBI's homologene database? You can get more or less one to one orthologs from many species. Here is an example of [GAPDH gene][1]. [1]: https://www.ncbi.nlm.nih.gov/gene/2597/ortholog/?scope=117570 ...
written 9 hours ago by genomax ♦ 78k
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Comment: C: bbmap.sh: line 352 /random number/ Killed
... Do you actually have `*` in the directory names above? Wonder if those are causing issues. bbmap.sh -Xmx40g threads=4 in1=sample_r1.fastq in2=sample_r2.fastq out=sample_bbmapped.bam ref=your_reference.fa ...
written 9 hours ago by genomax ♦ 78k
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Comment: C: how to map NCBI protein IDs to assembly IDs
... Use `ADD COMMENT/ADD REPLY` when responding to existing posts to keep threads logically organized. Following should get the GenBank ID. $ esearch -db nuccore -query "GS601_10170" | elink -target assembly | esummary | xtract -pattern DocumentSummary -element Genbank GCA_010091945.1 ...
written 12 hours ago by genomax ♦ 78k
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Answer: C: how to map NCBI protein IDs to assembly IDs
... You could use [Entrez-direc][1]t and the locus tag like this: $ esearch -db nuccore -query "GS601_10170" | elink -target assembly | esummary | xtract -pattern DocumentSummary -element AssemblyAccession GCF_010091945.1 That protein ID is from IPG database and harder to map back to a unique ...
written 14 hours ago by genomax ♦ 78k
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Answer: A: Non mapping sequences in genome
... If you were using `bbmap.sh` (aligner from [BBMap package][1]) then you can collect unmapped sequences using `outu=` option. Something like bbmap.sh in1=R1.fq.gz in2=R2.fq.gz outu1=R1_unmap.fq.gz outu2=R2_unmap.fq.gz .... Some other aligner will also allow you to do this during mapping. Otherw ...
written 19 hours ago by genomax ♦ 78k
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Comment: C: Best way to find all downloadable publicly available raw fastq files from SRA/GE
... That just looks like the [top level series accession][1] for multiple samples. If you look at the individual 90+ samples each of those has a SRA accession. [1]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96107 ...
written 19 hours ago by genomax ♦ 78k
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Comment: C: Best way to find all downloadable publicly available raw fastq files from SRA/GE
... > It looks like some datasets available only on GEO and not SRA Can you provide an example? ...
written 20 hours ago by genomax ♦ 78k
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Answer: C: Best way to find all downloadable publicly available raw fastq files from SRA/GE
... You can try `sra-explorer` ( https://sra-explorer.info/ ) from Phil Ewels. ...
written 23 hours ago by genomax ♦ 78k
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Answer: A: Extract fasta sequnces not matching a list
... You can use `faSomeRecords` from [Jim Kent's utils][1] for that. faSomeRecords - Extract multiple fa records usage: faSomeRecords in.fa listFile out.fa options: -exclude - output sequences not in the list file. [1]: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64 ...
written 23 hours ago by genomax ♦ 78k
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Comment: C: What to do with a bunch of Viral Genomes
... Since you selected these strains (which are similar) there is not much of a point in doing BLAST analysis. Instead, you can start doing a multiple sequence alignment with the sequences. If you are serious about learning then there are command line version of `MAFTT`, `T-COFFEE`, `Clustal` , `MUSCLE` ...
written 1 day ago by genomax ♦ 78k

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