User: akh22

gravatar for akh22
akh2240
Reputation:
40
Status:
New User
Location:
United States
Last seen:
4 weeks ago
Joined:
5 years, 6 months ago
Email:
a****@pitt.edu

Posts by akh22

<prev • 37 results • page 1 of 4 • next >
0
votes
0
answers
1.6k
views
0
answers
Comment: C: Adjust for covariates
... Could you explain why residual rather than fitted value for adjusted value ? Residual is observed - fitted so adjusted value (covariate corrected) should be fitted ? ...
written 28 days ago by akh2240
0
votes
1
answer
87
views
1
answer
Amazon AWS setup for the bioinformatic analysis particularly scRNAseq
... I am trying to setup EC2 Amanzon AWS Rstudio and Linux AMI for scRNAseq analysis, and I am curios to see what sort of set up are sufficient and cost-effective for the bioinformatic use. For Rstuio, I tried the Rstudio AMI (developed by Louis Aslett )and mainly run **Seurat (integration), Single ...
aws rstudio scrnaseq written 4 weeks ago by akh2240 • updated 4 weeks ago by Kevin Blighe59k
0
votes
0
answers
97
views
0
answers
Comment: C: Getting a GTF of expressed repeat annotation from Ensembl
... Thanks. I think I got it. I followed the link you posted and the answer had the clue. It is included in a dan folder in the Fasta DNA dump. According to README, `dna` is unmasked DNA sequence and `dna-rm` corresponds to hand masked genomic DNA whereas `dan-sm` is the soft masked DNA sequence. I ...
written 4 weeks ago by akh2240
0
votes
0
answers
97
views
0
answers
Getting a GTF of expressed repeat annotation from Ensembl
... Hi, I can generate and download GTF of repeated sequence (mm10) from a USCD table browser by using a RepeatMasker track. Can anybody point me in the right direction to do this with Ensembl browser ? Also, Ensembl has a hand-made, (rather than using RepatMaskter) repeated sequence list ?, and i ...
sequence rna-seq written 7 weeks ago by akh2240
0
votes
2
answers
9.2k
views
2
answers
Comment: C: How to adjust data for "continuous" covariates ?
... @Bioinformatics_NewComer, Did you figure this one out ? Using residual as adjusted value does not make sense to me. Thanks. ...
written 9 weeks ago by akh2240
2
votes
1
answer
1.0k
views
1
answer
Seurat3: RNA vs SCT assays for DotPlot
... HI, I am bit confused the use of RNA vs SCT assays for DGE analysis, and wondering if anybody who uses Seurat to shed a light. I've been preforming a Seurat3 integration method with SCTranform by simply following their vignette. According to some discussion and the vignette, a Seurat team indi ...
seurat3 scrnaseq written 9 months ago by akh2240 • updated 9 months ago by jared.andrews075.5k
0
votes
2
answers
418
views
2
answers
Answer: A: Sea of Ns in downloaded mm10 from NCBI and GRCm38.p6 primary sequence from Ensem
... My bad. There was nothing wrong with the sequence. It turned out that I was using an OSX wrapper fo gzip and sometimes it corrupts .gz file for some unknown reason in my Mac. I manually uncompressed file and they are fine. Thanks. ...
written 9 months ago by akh2240
1
vote
2
answers
418
views
2
answers
Sea of Ns in downloaded mm10 from NCBI and GRCm38.p6 primary sequence from Ensemble
... I download mouse ref genomes, mm10(GCF_000001635.26_GRCm38.p6_genomic.fna.gz)NCBI and GRCm38.p6 (Mus_musculus.GRCm38.dna.primary_assembly.fa,gz) from Ensembl sites and looked at the sequence inside. Chr. 1 through 19 had all Ns. Only Mt have valid nucleotide sequences. I'd appreciate if anybody ...
reference genome rna-seq written 9 months ago by akh2240
0
votes
0
answers
204
views
0
answers
Model Matrix Interacting model
... I am using edgeR's glm approach to determine dge of two groups, wide type (WT) and transgenic (TR) mice, both of which receive four sets of treatment, A, B, A+B, and saline) as follows, mouse treatment 1: TR A+B 2: TR A 3: TR B 4: TR ...
next-gen rna-seq edger model/design matrix written 10 months ago by akh2240
0
votes
1
answer
1.4k
views
1
answers
Answer: A: Loading 10x data into Monocle 3
... I figured it out. It was simple. CellRanger uses mm10 as a mouse ref, genome, and all I have to do is to change the name of folder, GRCm38 to mm10. This did it. ...
written 11 months ago by akh2240

Latest awards to akh22

Popular Question 4 weeks ago, created a question with more than 1,000 views. For A strategy to get Bacterial NCBI RefSeqs excluding contigs in an one file
Popular Question 7 months ago, created a question with more than 1,000 views. For Loading 10x data into Monocle 3
Popular Question 5.3 years ago, created a question with more than 1,000 views. For A strategy to get Bacterial NCBI RefSeqs excluding contigs in an one file

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1477 users visited in the last hour