User: mariafirulevabio

Reputation:
40
Status:
New User
Location:
Last seen:
2 months ago
Joined:
9 months, 2 weeks ago
Email:
m***************@gmail.com

Posts by mariafirulevabio

<prev • 20 results • page 1 of 2 • next >
0
votes
0
answers
164
views
0
answers
Comment: C: Get original format information from SRA metadata
... I mean Data access -> Original format -> **TenX** in "Type" column, using my link. ...
written 4 months ago by mariafirulevabio40
0
votes
0
answers
164
views
0
answers
Get original format information from SRA metadata
... Dear all, Consider I want to get the original format for certain SRR (e.g., [this one][1]). I have SRAmetadb.sqlite. What exactly should I do in this case? Best wishes, Maria [1]: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR7536866 ...
sra sqlite3 sradb pysradb metadata written 4 months ago by mariafirulevabio40
0
votes
0
answers
153
views
0
answers
Get single-cell technology used for certain sample
... Dear all, Consider I have a large matrix with SRS, SRX, SRA, GSM, direct links to fastq.gz and some other fields. This matrix includes only scRNA-seq experiments for *Mus musculus*. I want to know which single-cell technology used for certain sample, e.g., 10xv2, 10xv3, DropSeq, SCRBSeq, etc. Beca ...
geo metadata gsm scrnaseq sra written 4 months ago by mariafirulevabio40
0
votes
1
answer
253
views
1
answers
Comment: C: Extract GEO for certain experiment type
... Hi genomax, Thanks for your advice. I suppose I should not only 'scRNAseq' but other terms because after intersection my list (1315 elements) with the got list from I found only 4 common accession numbers. Could you prompt me how I can get direct links to files that correspond to the accession num ...
written 7 months ago by mariafirulevabio40
2
votes
1
answer
253
views
1
answer
Extract GEO for certain experiment type
... Dear all, Suppose I have a big list of GEO's corresponding certain experiment type (e.g., sc-RNA-seq). How can I extract all GEO's for target experiment type (sc-RNA-seq, in this case) and, after comparison all available GEO with my list, extract direct links for files which are presented in selec ...
geo gsm geo accession bioconductor written 7 months ago by mariafirulevabio40
2
votes
1
answer
178
views
1
answer
Unindexed clusters: Illumina
... Dear all, Could you please explain the concept of "Unindexed clusters" as a result of Illumina sequencing? What leads to the appearance of such clusters? How do I interpret a high or low percentage of such clusters in my results? Also, what "filters" are appealed to clusters that are marked "PF" in ...
ilumina clusters illumina index written 7 months ago by mariafirulevabio40 • updated 7 months ago by genomax78k
0
votes
1
answer
3.2k
views
1
answers
Answer: A: tumor only variant calling tools
... This [paper][1] provide information about different variant callers, including variant callers with available tumor-only mode. [1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5852328/ ...
written 8 months ago by mariafirulevabio40
1
vote
1
answer
298
views
1
answers
Comment: C: Target cancer sequencing: can't find database with raw data and related publicat
... Thanks, Kevin! I suppose it is better for me to choose a target panel which doesn't overlap complicated regions (repeats, high GC-content sequences, etc). ...
written 8 months ago by mariafirulevabio40
0
votes
1
answer
298
views
1
answers
Answer: A: Target cancer sequencing: can't find database with raw data and related publicat
... Since I've not found the answer, I guess these links ([post][1], [paper][2]) will be useful for someone with the same aims. I've decided to use a mixture of two Genome in a Bottle samples (truth set is available) for somatic variant calling validation. There is an option to choose a desired gene pa ...
written 8 months ago by mariafirulevabio40
1
vote
0
answers
352
views
0
answers
Imputation of scRNA-seq data
... There are several tools for imputation of scRNA-seq data, most of them have released in 2018-2019. Since these programs were announced recently, it is complicated to find info about user' choice, except several articles for comparison several of these tools (e.g., [this][1]). Will you provide me you ...
scrna-seq imputation rna-seq written 8 months ago by mariafirulevabio40

Latest awards to mariafirulevabio

Supporter 7 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1948 users visited in the last hour