User: Triple Nipple

Reputation:
0
Status:
New User
Last seen:
4 weeks ago
Joined:
1 year ago
Email:
m*************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by Triple Nipple

<prev • 8 results • page 1 of 1 • next >
1
vote
1
answer
187
views
1
answer
Converting VCF to CSV file
... Is there a tool that converts a VCF file annotated with SnpEFF and SnpSift to a csv file? I usually have multiple samples in VCFs so the ideal would be producing one row per variant and the sample column to show the genotype/AD/GQ/DP. Thanks! ...
vcf wgs whole-genome sequencing csv genome written 4 weeks ago by Triple Nipple0 • updated 4 weeks ago by Kevin Blighe65k
1
vote
1
answer
108
views
1
answer
Raw reads from Expression Atlas
... Hi, Is there a way to get the raw reads, fastq files of RNAseq of samples from the Expression Atlas (https://www.ebi.ac.uk/gxa/home)? I searched the Expression Atlas documentation and the internet but I didn't find anything. Thank you! ...
next-gen expression-atlas rna-seq written 5 months ago by Triple Nipple0
1
vote
1
answer
180
views
1
answer
Getting information about shortening or lengthening of UTRs from RNAseq data
... How can I get information about the length of UTR sequence from RNAseq data that aligned to reference? I need to know for each transcript if the 3UTR got longer or shorter. Is this possible? Note: In the ensembl .gtf file the UTRs were annotated, I managed to find their expression, but can I get ...
assembly rna-seq written 8 months ago by Triple Nipple0 • updated 8 months ago by mmfansler350
0
votes
0
answers
243
views
0
answers
Comparing multiple groups within multiple Cell Lines in DESEQ2
... Hello, I'm using DESEQ2 to calculate differential expression of genes. My data can be best seen through my metadata file which looks like this: projectname Line Treatment 1 LineX DoseA 2 LineX DoseA 3 LineX DoseB 4 LineX DoseB 5 LineX Untreat ...
R deseq2 chip-seq rna-seq written 9 months ago by Triple Nipple0
0
votes
0
answers
154
views
0
answers
Choosing uniquely differentially expressed genes
... Hello, I have two DESEQ2 analysis results between samples. The first one is for a feature A (in gtf), and the second one for feature B. Both Deseq2 analysis are done between the same samples. I want to get a list of genes that are differentially expressed for A, but are not differentially express ...
deseq2 rna-seq written 10 months ago by Triple Nipple0
2
votes
1
answer
400
views
1
answer
3' UTRs GTF file
... Hello, I have aligned RNAseq data to reference genome and now I have a .bam file. I want to check for the expression of the 3' UTR region of the transcripts. For this I need a .gtf file that has annotates 3' UTR regions of transcripts. How is it possible to get such file from ensembl (the sequencin ...
gtf utr mir expression written 10 months ago by Triple Nipple0 • updated 10 months ago by Asaf8.4k
2
votes
1
answer
521
views
1
answer
How to get transcripts counts from STAR
... Hello, After successful runs of STAR, in the ReadsPerGene.out.tab file, I only have counts of Genes (ENSG/ENSMUSG) and I don't have counts of transcripts (ENST/ENSMUST), which I need. My STAR index genome was obtained by reference genome from ENSEMBL and the .gtf annotation files were achieved fr ...
deseq2 star rna-seq written 10 months ago by Triple Nipple0 • updated 10 months ago by h.mon31k
2
votes
2
answers
255
views
2
answers
Assembly of DNA from .bam file
... From a .bam file of RNA sequence reads that are aligned to a mouse reference genome, how can I get a new bam file that contains this same genome assembled in reference to mm10 reference genome. If I made things clear I need to get one long read sequence for each location and not many reads like it's ...
genome assembly bam rna-seq sequence written 12 months ago by Triple Nipple0 • updated 12 months ago by swbarnes28.6k

Latest awards to Triple Nipple

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: 1579 users visited in the last hour