Tag: Salmon

Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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python – Missing input files after defining them in function

I am trying to do QC on RNAseq data that is tarballed. I am using Snakemake as a workflow manager and am aware that Snakemake does not like one-to-many rules. I defining a checkpoint would fix the problem but when I run the script I get this this error message…

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RNA-seq analysis cloud server

RNA-seq analysis cloud server 1 Hi all, I have some RNA-seq of mice (around 200GB) and I want to perform a RNA-seq analysis (including QC, mapping, quantification, differential expression analysis). But I don’t know how to choose a server. Could anyone can tell me to process such a dataset, how…

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The 2021 Good Tech Awards

In the tech industry, 2021 was a year of profits and pivots. Thanks in part to the pandemic and the digitization of our lives, all of the big tech companies got bigger. Facebook changed its name to Meta, Jeff Bezos went to space, Jack Dorsey left Twitter and Silicon Valley…

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Help needed for Ensembl Gene ID conversion for RNA-seq data

Hello All, I am new to the RNA-seq world and especially new to the bioinformatics side. We recently completed a RNA-seq experiment (total RNAs) on human samples and we used illumina’s Dragen RNA pipeline which generated salmon gene count (.sf) output files. In the files, the gene ID is in…

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Tximport in usegalaxy

Tximport in usegalaxy 0 Devon Ryan: Please help in resolving this issue. How to use tximport in usegalaxy to convert transcript ID(DESEQ2-SALMON) to gene ID. I want to get gene ids from the results of deseq2(salmon) . Which GTF should be used for tximport. Iam getting the following error in…

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Quick questions about Alevin and AlevinQC

I have just started using Alevin and I have few basic queries. And I am asking this because I couldn’t find it in the documentation How to know how many reads are uniquely mapping and how many are multi mapping when doing quantification with Alevin. The alevin_meta_info.json says Number of…

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Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

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Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 CAS  PubMed  PubMed Central  Article  Google Scholar  Alexander DH, Shringarpure SS, Novembre J, Lange K (2015) Admixture 1.3 software manual. UCLA Hum Genet Softw Distrib, Los Angeles Google Scholar  Angert AL, Bontrager…

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Transcripts mapping using Salmon

Transcripts mapping using Salmon 0 Hi all, We have recently conducted total RNA-seq (~200M reads) and mRNA-seq (~100M reads) in the same samples. Following the RNA-seq, we used Salmon selective alignment (SA) to align the reads to the Ensembl human transcriptome. This resulted in a comparable number of reads (~40M)…

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Differential splicing/transcript usage/isoform analysis of iCell8 (SMART-seq v2) full transcriptome single cell data in conjunction with Seurat

Differential splicing/transcript usage/isoform analysis of iCell8 (SMART-seq v2) full transcriptome single cell data in conjunction with Seurat 0 Dear all, I am currently analyzing single-cell data gathered using the iCell8 platform (Takara) that captures full transcripts using the SMART-seq v2 chemistry. The official pipeline by Takara (CogentAP) uses STAR for…

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geneiD-genetranscript annotations

Hello, Trying to generate a frame with 2 columns: transcript_id and gene_id, in LINUX (gtf from esembl) grep -P -o ‘ESNCAGd{11} Equus_caballus.EquCab3.0.104.gtf’ > ensecag.txt grep -P -o ‘ESNCATd{11} Equus_caballus.EquCab3.0.104.gtf’ > ensecat.txt wc -l enseca* # To see if both files have the same length They are not the same length:…

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Transcriptional noise detection and Salmon TPMs

Transcriptional noise detection and Salmon TPMs 1 Hello, I’m analysing RNA-seq data from two datasets (from healthy samples) and created a unique GTF file to identify new isoforms by using StringTie. Then I used Salmon to estimate their TPMs, but I have some questions hoping anyone can help me: 1)…

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Bioconductor Forum

James W. MacDonald 57k 1 week, 5 days ago United States Answer: Biomart’s getBM returns no genes for an existing GO-term in grch38, and less the Michael Love 33k 1 week, 6 days ago United States Answer: Normalizing 5′ Nascent RNA-seq data to identify differentially expressed transcr Kevin Blighe 3.3k 2 weeks, 2 days ago Republic…

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When importing my quant.sf files into R using tximport, should I set ‘ignoreTxVersion’ to True or False?

Hello, I’m working through my first batch of RNA-Seq analysis and unfortunately I don’t have an experienced bioinformatician to work with. My question is regarding tximport of my quant.sf files into R. I have been working with the EquCab3.0 reference transcriptome from NCBI to generate these quant.sf files, but I…

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How do I match my transcript ID’s from NCBI to the corresponding gene ID’s to enable tximport into R?

How do I match my transcript ID’s from NCBI to the corresponding gene ID’s to enable tximport into R? 2 Hi all, New to RNA-Seq analysis and I tried to find an answer to this elsewhere. I have performed salmon alignment on my pair-end fastq files which has generated the…

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Senior Programmer Analyst/Bioinformatics in New York, NY for Columbia University

  Job Seekers, Welcome to HERC Jobs Senior Programmer Analyst/Bioinformatics Columbia University Columbia University Job Type: Officer of Administration Bargaining Unit: Regular/Temporary: Regular End Date if Temporary: Hours Per Week: 35 Salary Range: Commensurate with experience  …

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Problems with fragment length distribution output with Salmon

Problems with fragment length distribution output with Salmon 1 Hi all, New to RNA-Seq and I’m struggling with my Salmon alignment output. I tried to find an answer to this question on older posts but I couldn’t locate any other discussions, so apologies in advance if this has been covered…

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