User: noeD

gravatar for noeD
noeD70
Reputation:
70
Status:
Trusted
Location:
Last seen:
5 days, 3 hours ago
Joined:
10 months ago
Email:
n************@gmail.com

Posts by noeD

<prev • 43 results • page 1 of 5 • next >
0
votes
0
answers
86
views
0
answers
locateVariants missing some mutation site
... Hello! I am using Variant Annotation package from Bioconductor to annotate my variant but it missed some variants in the output. For example, in `var` I have the following mutation site : CHROM POS REF ALT 9751 chr6 41184897 G A I used `GRanges` for the genomic locati ...
R bioconductor variant annotation written 10 days ago by noeD70
0
votes
1
answer
103
views
1
answers
Comment: C: Cosmic Database using BioMart
... Thank you for your reply. But is it possible to download the database for INDEL mutations? Thank you in advance ...
written 11 days ago by noeD70
4
votes
1
answer
103
views
1
answer
Cosmic Database using BioMart
... Hello! I have read that with BioMart package in R it is possible to download the cosmic database. Unfortunately I didn't understand how to do it. If I use listMart() I see only ensemble-database.. I have tried with listMart(host=http://cancer.sanger.ac.uk/cosmic), but it didn't work... Thank you i ...
R biomart cosmic written 12 days ago by noeD70 • updated 12 days ago by Emily_Ensembl13k
0
votes
1
answer
232
views
1
answers
Comment: C: featuresCount -s 2 option
... I apologize for my stupid question.. but if I have paired-end reads, it doesn't mean that the library is directional? Thank you in advance ...
written 11 weeks ago by noeD70
0
votes
1
answer
232
views
1
answers
Comment: C: featuresCount -s 2 option
... Thank you for your reply. How can I confirm it? Furthermore, is it normal to obtain that percentage of assigned reads? Thank you in advance for your help! ...
written 11 weeks ago by noeD70
6
votes
1
answer
232
views
1
answer
featuresCount -s 2 option
... Hello! :) I have paired-end RNA-seq data aligned by STAR, I used featuresCount in order to get read summarization.(I know that STAR can give the count, but I would like to try with featuresCount). I don't understand why if I use the "-s 2" option I obtained a lower number of assigned read than with ...
featurescount rna-seq written 11 weeks ago by noeD70 • updated 11 weeks ago by Devon Ryan71k
0
votes
0
answers
113
views
0
answers
Comment: C: miRNA-featuresCount: Unassigned_Ambiguity high value
... Thank you for your help! This is the output: Assigned 37650812 Unassigned_Unmapped 2398401 Unassigned_MappingQuality 0 Unassigned_Chimera 0 Unassigned_FragmentLength 0 Unassigned_Duplicate 0 Unassigned_MultiMapping 0 Unassigned_Secondary 0 Unassigned_Nonjunction ...
written 11 weeks ago by noeD70
0
votes
3
answers
272
views
3
answers
Comment: C: extract subset of sequence
... https://www.biostars.org/p/142705/ or zcat file.fastq.gz | head -4*#readYouWant > new.fastq ...
written 11 weeks ago by noeD70
0
votes
2
answers
9.7k
views
2
answers
Comment: C: Bowtie2 parameters for best alignment
... Hi! why it is better to use --very-sensitive than --very -sensitive-local in case of trimmed reads? Thank you in advance! ...
written 12 weeks ago by noeD70
0
votes
1
answer
282
views
1
answers
Comment: C: featuresCount order sam file?
... I have tried to use featuresCount sorting the read and without doing it... I obtained the same result... ...
written 12 weeks ago by noeD70

Latest awards to noeD


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1443 users visited in the last hour