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protein - lncRNA interactions

rna-seq written 3 hours ago by glady • 260

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RNAseq analysis of interspecies hybrid

assembly alignment rna-seq written 3 hours ago by alicelouiseflint • 0

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Mapping different mouse strains to mm10

hybrid-mouse scrna rna-seq written 6 hours ago by Assa Yeroslaviz • 1.4k

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help clarify ways to measure coverage in RNA-Seq libraries

coverage rna-seq written 12 hours ago by DataFanatic • 240

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problem with fastq dump

fastq dump prefetch rna-seq written 9 hours ago by mo.ghasemi717 • 0

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problem with trimmomatic

gene trimmomatic rna-seq written 2 days ago by mo.ghasemi717 • 0 • updated 14 hours ago by Lesley Sitter • 530

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GFF problem - gtf_to_fasta (Tophat) outputs only 2 sequences from 70 entries in GFF?

gtf tophat gff rna-seq written 5.1 years ago by manekineko • 130 • updated 14 hours ago by Biostar ♦♦ 20

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Job: Postdoctoral scholar studying tumor genetics and epigenetics at UCSF

next-gen epigenetics job rna-seq written 14 hours ago by David Quigley ♦ 11k

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Differential Gene Expression with Replicates for some of the samples

deseq2 rna-seq edger limma written 1 day ago by rezaeir75 • 10 • updated 17 hours ago by Ali T. A. • 20

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Recent Replies

A: Replace matching sections of two fastas by Pierre Lindenbaum ♦ 129k
- [linerize both fasta files][1] - remove the '/rc' suffix with `sed` - use `sort` to sor...
C: Using Limma in R to get log2 fold change data for GSE series data, want to get r by sslimb95 • 0
Yes it is. https://www.genecards.org/cgi-bin/carddisp.pl?gene=A1BG AIBG gene's external id which...
C: filtered tab delinited file with awk by Pierre Lindenbaum ♦ 129k
awk '($13>=0.5)' input > output
C: DESeq2 compare all levels by krushnach80 • 810
okay that sounds simple and straightforward
C: filtered tab delinited file with awk by Mehmet • 570
I guess FPKM is the 13th column. if so, you can print transcripts that have FPKM values greater t...
A: Using Limma in R to get log2 fold change data for GSE series data, want to get r by Alex Nesmelov • 110
You can recount transcription for genes from bam files, using htseq2 with '-t gene' option. For t...
C: How to assemble mulitple paired-end files? by genomax ♦ 87k
> I want to assemble two paired-end read files with each other. I don't know what exactly you...
C: randomly shuffle BAM file by alanh • 80
It appears that if you run `samtools bamshuf` on more recent versions of samtools, it translates ...
C: Fast download of FASTQ files from the European Nucleotide Archive (ENA) by andreipro87 • 0
great tool, super useful and works like a charm, kudos!
C: Finding unique variants in a vcf by RamRS ♦ 28k
Have you looked at `bcftools view -x`? https://samtools.github.io/bcftools/bcftools.html#view
C: How to assemble mulitple paired-end files? by audrey.durand • 0
Yes!! Perfect, it works great! Thank you so much for your help Assa Yeroslaviz.
C: Finding unique variants in a vcf by Pierre Lindenbaum ♦ 129k
see GATK [selectvariants][1] with a [JEXL expression][2]. e.g: !vc.getGenotype("sample1").i...

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