Admin: genomax

gravatar for genomax
genomax78k
Reputation:
77,980
Status:
Trusted
Location:
United States
Last seen:
9 hours ago
Joined:
4 years, 8 months ago
Email:
g*******@gmail.com

Posts by genomax

<prev • 13,852 results • page 1 of 1386 • next >
0
votes
1
answer
45
views
1
answers
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 genomax78k
0
votes
0
answers
70
views
0
answers
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 genomax78k
0
votes
1
answer
37
views
1
answers
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 genomax78k
0
votes
1
answer
37
views
1
answers
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 genomax78k
1
vote
1
answer
50
views
1
answers
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 genomax78k
0
votes
1
answer
66
views
1
answers
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 genomax78k
0
votes
1
answer
66
views
1
answers
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 genomax78k
3
votes
1
answer
66
views
1
answers
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 genomax78k
2
votes
1
answer
62
views
1
answers
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 genomax78k
1
vote
0
answers
70
views
0
answers
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 genomax78k

Latest awards to genomax

Teacher 21 hours ago, created an answer with at least 3 up-votes. For C: Best way to find all downloadable publicly available raw fastq files from SRA/GE
Scholar 21 hours ago, created an answer that has been accepted. For C: Best way to find all downloadable publicly available raw fastq files from SRA/GE
Commentator 1 day ago, created a comment with at least 3 up-votes. For C: Corona Virus- Sequence alignment-Phylogeny analysis
Scholar 10 days ago, created an answer that has been accepted. For A: Single-end sequencing versus paired-end
Scholar 11 days ago, created an answer that has been accepted. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Scholar 12 days ago, created an answer that has been accepted. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Popular Question 12 days ago, created a question with more than 1,000 views. For NovaSeq from Illumina (updated info)
Commentator 14 days ago, created a comment with at least 3 up-votes. For C: Please help me enter this world of bioinformatics!
Appreciated 15 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Appreciated 16 days ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Teacher 16 days ago, created an answer with at least 3 up-votes. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Scholar 16 days ago, created an answer that has been accepted. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Teacher 17 days ago, created an answer with at least 3 up-votes. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Scholar 17 days ago, created an answer that has been accepted. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Teacher 18 days ago, created an answer with at least 3 up-votes. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Teacher 19 days ago, created an answer with at least 3 up-votes. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Scholar 20 days ago, created an answer that has been accepted. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Teacher 20 days ago, created an answer with at least 3 up-votes. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Scholar 23 days ago, created an answer that has been accepted. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Scholar 26 days ago, created an answer that has been accepted. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Appreciated 4 weeks ago, created a post with more than 5 votes. For A: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Scholar 4 weeks ago, created an answer that has been accepted. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: How to get SNP id (rsid) from this input "myGene 1234C>A" ?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1526 users visited in the last hour