User: jamespower

gravatar for jamespower
jamespower30
Reputation:
30
Status:
New User
Location:
Last seen:
6 months, 3 weeks ago
Joined:
1 year, 7 months ago
Email:
j*********@gmail.com

Posts by jamespower

<prev • 20 results • page 1 of 2 • next >
0
votes
0
answers
288
views
0
answers
Comment: C: List of TCGA genes differentially expressed in normal versus tumor
... Thank you Kevin for your reply. Yes, time constrains, and the fact that I was hoping there were gene lists available already, since it seems like a very common and possibly simple analysis that doesn't need to be re-done by everyone... ...
written 6 months ago by jamespower30
0
votes
0
answers
288
views
0
answers
List of TCGA genes differentially expressed in normal versus tumor
... Hi, I am looking for a gene list with differentially expressed genes in a particular tissue, using normal versus tumor samples (for example as reported in https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071462#s3). The TCGA website has RNA-Seq data on tumor samples, but I was j ...
tcga rna-seq written 6 months ago by jamespower30
0
votes
0
answers
434
views
0
answers
Comment: C: Plink Error: Duplicate ID 'chr:pos:A1:A2' generated by --set-missing-var-ids
... Thanks! Using plink2, with `--set-missing-var-ids @:#\$r:\$a`, and `--new-id-max-allele-len 23 missing` works great! ...
written 7 months ago by jamespower30
3
votes
0
answers
434
views
0
answers
Plink Error: Duplicate ID 'chr:pos:A1:A2' generated by --set-missing-var-ids
... Hi, I am trying to work with the 1000Genomes data starting from the vcf file, which has missing IDs. So, I thought of adding the flag `--set-missing-var-ids @:#:\$1:\$2`, but this gives me the error: Error: Duplicate ID generated by --set-missing-var-ids. So I guess first we want to find ...
duplicates missing id plink written 7 months ago by jamespower30 • updated 7 months ago by RamRS24k
6
votes
1
answer
251
views
1
answer
How to combine RNA-Seq from Novaseq separated in lanes, after fpkm have been computed?
... Hi, I have been given two files with FPKM values computed on different lanes for the same sample, is it appropriate to sum the FPKM values by gene and sample across the different lanes? Thank you for any help ...
gene next-gen rna-seq written 9 months ago by jamespower30
0
votes
1
answer
501
views
1
answers
Comment: C: Format in vcf files in Geuvadis data not recognized
... Even if it says it as a warning, I cannot do certain operations such as extracting sample IDs (I update the last output for the error message). ...
written 14 months ago by jamespower30
5
votes
1
answer
501
views
1
answer
Format in vcf files in Geuvadis data not recognized
... Hi, I have downloaded Geuvadis genotypes from: https://www.ebi.ac.uk/arrayexpress/files/E-GEUV-1/GEUVADIS.chr22.PH1PH2_465.IMPFRQFILT_BIALLELIC_PH.annotv2.genotypes.vcf.gz And I am trying to recreate vcf files with only the European samples using bcftools, but when I try bcftools view --samp ...
vcf samtools format bcftools geuvadis written 14 months ago by jamespower30 • updated 14 months ago by Pierre Lindenbaum122k
0
votes
3
answers
460
views
3
answers
Comment: C: What is the best and latest package/software for post-processing of Hi-C (Chromo
... Thank you, I think HiGlass is mostly to view the data, while I was wondering about the pipeline/packages used for calling an interaction significant and overlapping with GWAS SNPs. ...
written 17 months ago by jamespower30
8
votes
3
answers
460
views
3
answers
What is the best and latest package/software for post-processing of Hi-C (Chromosome Conformation Capture)?
... I am new to Hi-C data analyses and I am looking for the latest package and references on how to overlap this type of data with GWAS and genes. Thanks for suggestions! ...
gene R next-gen hic gwas written 17 months ago by jamespower30 • updated 10 months ago by afli190
0
votes
0
answers
1.0k
views
0
answers
Comment: C: QQ plots for eqtl data
... Hi Fabio, thanks for your feedback! I have used matrixEQTL. That is worrying indeed, especially happening even after filtering rare SNPs before the association... is there any way you may know of filtering those cases further, or maybe another software that better controls for this? (or did you just ...
written 17 months ago by jamespower30

Latest awards to jamespower

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: 1667 users visited in the last hour