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Looking for Recommendations: whole Adult male Danio rerio RNAseq data

sra daniorerio mapping rna-seq written 5 months ago by jaqx008 • 50

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How to (and where) download Zebrafish Reference Genome (other than Ensembl or USCS)?

genome fasta zebrafish reference daniorerio written 10 months ago by realnewbie • 10 • updated 10 months ago by WouterDeCoster ♦ 40k

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Recent Replies

A: How to make batch univariate cox analysis for list by Kevin Blighe ♦ 45k
My Bioconductor package, *RegParallel*, will do this for you, i.e., it can test each gene indepen...
C: Extract reads from a bam file to have two fastq files with the same number of re by genomax ♦ 69k
4596 + 0 singletons (0.08% : N/A) Some are explained by those.
C: Extract reads from a bam file to have two fastq files with the same number of re by macielrodriguez2 • 20
It worked great!!! Thank you so much genomax!!! But what are these reads? According to my flags...
C: Get Gene symbols by qicaibiology • 10
That is great if the author can help to make it through. I will shared my notes/process on each s...
A: Is it possible to directly convert fastq to CRAM ? by Charles Warden ♦ 7.0k
While some programs require uncompressed .fastq files, many/most will accept .fastq.gz files. Cr...
C: Is it possible to directly convert fastq to CRAM ? by genomax ♦ 69k
For reference [manual page][1] appears to say otherwise. Or should that additionally say "not req...
C: Get Gene symbols by jared.andrews07 • 2.7k
Yes, as I said, this will cause that error due to the duplicate row names. You need to figure out...
C: I want to know if there is reference for brain cell types by jared.andrews07 • 2.7k
There are about 9 billion different cell types in the brain, so that sounds like quite the task. ...
A: Is it possible to directly convert fastq to CRAM ? by jkbonfield • 120
While CRAM is indeed much smaller than BAM, its primary benefit is when using aligned data so you...
C: Pipe SamToFastq, BWA mem not working by ATpoint ♦ 19k
Ok, on Mac I sometimes had issues with non-writable stdout. As for the character limit, just add ...
C: Help making a blast database with longer sequence IDs by ravila • 0
Thanks! That solved the issue.
C: Augustus output (GFF file) to Anvi`o by Juke-34 • 2.2k
Do you use the option `—gff3` in Augustus? Because is you use the GTF output it is a bit wierd ...

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