User: sandeep.amberkar18

Reputation:
50
Status:
Trusted
Location:
Last seen:
1 week, 2 days ago
Joined:
2 years, 12 months ago
Email:
s*****************@gmail.com

Posts by sandeep.amberkar18

<prev • 12 results • page 1 of 2 • next >
0
votes
0
answers
141
views
0
answers
Comment: A: Genes With "." in Their Names
... In my experience, they're RNA polymerase or those starting with the LOC string but as Pierre mentioned above, it's best to provide an example to help you out. ...
written 19 days ago by sandeep.amberkar1850
1
vote
1
answer
84
views
1
answers
Comment: C: STAR index/alignment error : no exons found
... Got it, thanks! Just wanted to be sure about the g-dna as reference. ...
written 5 weeks ago by sandeep.amberkar1850
2
votes
1
answer
84
views
1
answer
STAR index/alignment error : no exons found
... Hi, I've some mouse tumour transcriptomic data (3' Quantseq), on which I want to do a differential expression analyses between treatment and control. I'm using STAR aligner to map the reads but I had the same error during index creation and mapping: Here's what I tried: `STAR --runMode genomeGene ...
star rna-seq written 5 weeks ago by sandeep.amberkar1850 • updated 5 weeks ago by caggtaagtat1.2k
0
votes
1
answer
273
views
1
answers
Comment: A: Salmon only processes human reads from PDX data
... @jrleary - While using Salmon for your use case of PDX samples, which reference do you use? Separate references for mouse and human or a combined reference? I have a similar scenario and I could use your help. Thanks in advance. ...
written 3 months ago by sandeep.amberkar1850
0
votes
1
answer
245
views
1
answers
Comment: C: Gene counts & expression level
... Thanks for the links, I think I've already read a few of them before posting. I wish I could be specific but the question posed on a weekly basis to me is as nebulous as it gets. ...
written 8 months ago by sandeep.amberkar1850
3
votes
1
answer
245
views
5 follow
1
answer
Gene counts & expression level
... Dear All, Here's a naive question which I've been asked by plant biologists often -- Can you tell me if a gene X is expressed in my RNAseq data set? I quickly rush to critic this approach as a gene count of 10 and is *expressed* but that won't count (pun intended) unless that gene is differentially ...
gene-count rna-seq written 8 months ago by sandeep.amberkar1850 • updated 8 months ago by h.mon30k
0
votes
1
answer
351
views
1
answers
Comment: C: DESeq2 nested effect with 5 variables
... Hi Leaodel, I'm sorry I should've been more clear about the exp. setup. The experiment consists of: - 2 Tissues -- Leaf, Crown - 2 Temperatures -- 21, 27 - 2 Time points -- AM, PM - 3 Dev Stages -- DS1, DS2, DS3 and 4 replicates for each. I posted only a subset of the coldata matrix, ...
written 12 months ago by sandeep.amberkar1850
0
votes
1
answer
351
views
1
answer
DESeq2 nested effect with 5 variables
... Hello All, I'm dealing with a rather complex RNAseq experiment that follows a nested structure of the tested variables that could be represented like this: SampleName tissue temp time dev_stage rep Sample1 crown 21 am ds1 rep1 Sample2 crown 21 am ds1 rep3 Sample3 crown 21 am ds1 re ...
R deseq2 rna-seq written 12 months ago by sandeep.amberkar1850 • updated 12 months ago by leaodel130
0
votes
2
answers
584
views
2
answers
Comment: C: Different filters for wheat in biomaRt package and website
... Thanks a lot Emily, I'll try it out! ...
written 18 months ago by sandeep.amberkar1850
8
votes
2
answers
584
views
2
answers
Different filters for wheat in biomaRt package and website
... Hello, I'm looking to download the Wheat TILLING & SNP data from Ensembl from the biomaRt package in Bioconductor. However, I've noticed that the filters available in biomart website are more than what you have in the Bioconductor package. For e.g. plantsDatabase <- useMart(biomart = 'p ...
ensembl biomart getbm written 18 months ago by sandeep.amberkar1850 • updated 18 months ago by Mike Smith1.5k

Latest awards to sandeep.amberkar18

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 927 users visited in the last hour