User: K

gravatar for K
K40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
8 months, 3 weeks ago
Joined:
2 years, 3 months ago
Email:
k**********@gmail.com

Posts by K

<prev • 45 results • page 1 of 5 • next >
0
votes
2
answers
202
views
2
answers
Comment: C: Extracting all possible annotations between two genomic coordinates
... I believe this is it: grch37 = useEnsembl(biomart="ensembl",GRCh=37,dataset="hsapiens_gene_ensembl") ...
written 8 months ago by K40
0
votes
2
answers
202
views
2
answers
Comment: C: Extracting all possible annotations between two genomic coordinates
... Quick follow up question I believe using this command below, it links to the latest genome reference GrCh38. genes_mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") Could you tell me how to change setting to the GRch37 Ensembl ? ...
written 8 months ago by K40
0
votes
2
answers
202
views
2
answers
Answer: A: Extracting all possible annotations between two genomic coordinates
... Thank you ! This is helpful -  I will start with Biomart. That's a good start.  ...
written 8 months ago by K40
0
votes
2
answers
202
views
2
answers
Extracting all possible annotations between two genomic coordinates
... Hello, I have a list of several base pair locations (each have a start and end base pair). Eg: Chr:17,  BasePair1: 26804211 , BasePair2: 26818676 And I am looking to find all possible annotations including gene name, known SNPs , microRNA etc between these two base pair locations (the region need ...
genomes written 8 months ago by K40
0
votes
2
answers
354
views
2
answers
Answer: A: subset from fastq file
... Thank you, just realized this was such a noob question.  ...
written 14 months ago by K40
0
votes
2
answers
354
views
2
answers
subset from fastq file
... Hello, I am trying to extract all reads from chromosome 1 (or any other chromosome) from a fastq file. The fastq file I have is from Illumina. I looked up ShortRead package, but I don't see an example for this in the vignette.  Could someone give advice ?  Thanks, K ...
fastq written 14 months ago by K40
0
votes
2
answers
255
views
2
answers
Answer: A: how to get transcript annotation (unique)
... Thank you ! This is great - I will decide what to do about the duplicates.  ...
written 19 months ago by K40
0
votes
2
answers
255
views
2
answers
how to get transcript annotation (unique)
... Hello, I have list of transcripts (From an RNA-seq quantification output), and I would like to annotate. I would like the annotation to have the following information (Gene name, NM id or some information about the mRNA, chromosome number, chr start and end) ucscid gene mrna refs ...
txdb written 19 months ago by K40
0
votes
2
answers
1.3k
views
2
answers
Answer: A: HTseq in bioconductor
... Thank you very much, I will try these out. ...
written 21 months ago by K40
1
vote
2
answers
1.3k
views
2
answers
HTseq in bioconductor
... Hello, I have been trying to install and run HTSeq-count python package on my windows machine since yesterday. I was able to install HTSeq and run a few of their examples. But when I try to run HTseq-count, it keeps telling me I am mssing a number of other python packages, and this has been going o ...
rnaseq bioconductor written 21 months ago by K40

Latest awards to K

Popular Question 21 months ago, created a question with more than 1,000 views. For example fastq file, sampleAnnotaition and Hairpin file for shRNAseq/EdgeR tool

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 258 users visited in the last hour