User: husensofteng

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husensofteng260
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Sweden
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1 week, 1 day ago
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2 years, 2 months ago
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Posts by husensofteng

<prev • 35 results • page 1 of 4 • next >
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Answer: A: Create a database of RefSeq genes
... The easiest way to get symbol and information on protein coding genes is through the NCBI gene resource page, here is a [link for refseq protein-coding genes][1] that you can re-generate with this query: "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND "srcdb refseq"[Prop ...
written 8 days ago by husensofteng260
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Comment: C: protein database and ensembl
... actually this info is in the `README` file located in the same ftp directory where you download your `.fa` files, e,g [here][1]. [1]: ftp://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/pep/README ...
written 16 days ago by husensofteng260
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Comment: C: protein database and ensembl
... `pep.all.fa` is used as reference. `pep.abinitio.fa` contains predictions made based on the genomic sequence and not any other experimental evidence therefore not all entries represent biologically real proteins. ...
written 16 days ago by husensofteng260
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Comment: C: To remove variants that encode for PE-PPE proteins from .vcf file
... It is not very clear what is the content of `pe_ppe.bed`. In case you want to exclude variants that overlap regions in the `pe_ppe.bed` file you can simply use `intersectBed` with the [`-v` flag][1]. [1]: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html#v-reporting-the-ab ...
written 22 days ago by husensofteng260
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Comment: C: Intron retension calculation (non-model organism)?
... as it was mentioned, `GTF` files usually don't contain introns. I have written a [gtf_plus_intron python script][1] to add introns to a `GTF` file: python gtf_plus_intron.py -i input.gtf -o output.gtf [1]: https://github.com/husensofteng/peptide-processor/blob/master/gtf_plus_intron.py ...
written 23 days ago by husensofteng260
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Comment: C: Whole Genome Sequencing Data Annotation
... [Sarek][1] which is a Nextflow pipeline is quite nice for WGS analysis. [1]: https://nf-co.re/sarek ...
written 26 days ago by husensofteng260
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Comment: C: I get this error while creating database on BLAST: BLAST Database creation error
... what blast version do you use? have you tried updating it? also, do you have write permission to the directory? ...
written 26 days ago by husensofteng260
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Comment: C: Getting coding sequence length
... if the species is annotated, you could get the [CDS in `fasta`][1] and count the number of bases there for your genes of interest. [1]: ftp://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/cds/ ...
written 4 weeks ago by husensofteng260
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Comment: C: Searching for introns within 5'UTRs
... May be you want to remove the `-wa` option in `bedtools intersect` if you only want the intron fragments that are located within 5'UTRs as you have stated above otherwise you get the entire intron sequence. ...
written 5 weeks ago by husensofteng260
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Comment: C: Biopython SeqIO.parse not functioning for all entries in a seq
... Try to install `Biopython` from the `github` source. It seems this issue is solved there, see [the discussion here][1]. [1]: https://github.com/biopython/biopython/issues/2844 ...
written 6 weeks ago by husensofteng260

Latest awards to husensofteng

Scholar 6 weeks ago, created an answer that has been accepted. For A: per sample mean coverage and standard deviation
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: convert genome file to transcriptome file
Popular Question 8 weeks ago, created a question with more than 1,000 views. For GATK Interval list for processing mouse genome WGS
Scholar 3 months ago, created an answer that has been accepted. For A: per sample mean coverage and standard deviation
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: convert genome file to transcriptome file

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