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227

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What would be the equivalent fasterq-dump options?

fasterq-dump written 9 weeks ago by requiem_data • 0

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202

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Extract SRA reads per RG using fasterq-dump

sra fasterq-dump dbgap written 12 weeks ago by MAPK • 1.7k

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132

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Number of reads in the downloaded fastq file

sra vdb-dump --info read count fasterq-dump written 12 weeks ago by kmkdesilva • 90

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1.5k

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SRA Toolkit: using fastq-dump vs fasterq-dump - discrepancies in output?

software error sratools fastq-dump fasterq-dump written 4 months ago by Hamish • 30

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1.8k

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6 follow

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Checking integrity of SRA downloaded fastq files

fastq-dump sequence sra toolkit fasterq-dump written 15 months ago by flyingbebegurl • 0 • updated 5 months ago by simplitia • 40

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422

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Mapping multiple SRR ID from same experiment

alignment srrid gsmid fasterq-dump fastq-dump written 15 months ago by singlecell • 0

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2.5k

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understanding the output files of fasterq-dump --split-files

fasterq-dump written 2.4 years ago by inbal.tzipermanl • 0 • updated 2.4 years ago by GenoMax ♦ 94k

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Recent Replies

C: DESeq2 Dispersion Estimates Curve Poor Fit? by lransom • 0
![DispEstsLocal][1] After looking into it some more, I tried setting the DESeq parameter fitType...
C: Filtering on the minor allele in VCFtools by bjwiley23 • 10
GATK indicates they do this for their [best practices](https://gatk.broadinstitute.org/hc/en-us/a...
C: bigwigs to reads in peaks by pt.taklifi • 60
thank you. that works
C: DESeq2 Dispersion Estimates Curve Poor Fit? by lransom • 0
Sorry, just fixed the image link. I'm trying to compare RNA from exosomes in Disease vs Heathy. I...
C: DESeq2 Dispersion Estimates Curve Poor Fit? by ATpoint ♦ 44k
Can you add code and some context, so what are the samples, in terms of groups, and how many repl...
C: How do i create and populates new sample columns based on values (samples barco by rpolicastro ♦ 3.2k
> P.S.: function pivot_wider seem to be from tidyr package and not dplyr. Nice catch, I edite...
C: How do i create and populates new sample columns based on values (samples barco by andresllucena • 0
I'm sorry, I will correct that. I used values from samples after the first one trying to improve ...
A: How do i create and populates new sample columns based on values (samples barco by rpolicastro ♦ 3.2k
There are values in your example output that don't appear in your example data, but I'll assume y...
A: WGCNA negative values by Kevin Blighe ♦ 69k
A negative FPKM value makes no sense, so, there is something wrong with your data processing step...
A: Identifying 5p and 3p in miRNA isoform expression data from TCGA for feature sel by andresllucena • 0
There is how i solve that: The 3p and 5p strands corresponds to these MIMAT IDs miRNA_region col...
C: Finding sets of Ribo-Seq, mRNA-Seq, and RNC-Seq data by seidel ♦ 7.1k
Have you tried the [GEO search interface][1] with those specific terms? I mean, have you checked ...
A: cellranger count error "Your reference does not contain the expected files, or t by leranwangcs • 20
To answer myself's question: I used a vdj database for my gene expression data. So when I switch ...

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