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Hi,
I am following the getting started tutorial (http://pachterlab.github.io/kallisto/10xstarting.html) for single cell RNAseq but when I get to the point:
Download the “human-mouse” transcripto…
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The Megakaryocyte_rep2 data is much smaller than the other samples. Is this intended? In https://www.ncbi.nlm.nih.gov/sra/?term=SRR549358 the original data of the two samples is about the same size. I…
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Hello,
I found a few contradicting posts in bioinformatics forums whether Megahit could be used or must not be used for metatranscriptome assemblies from microbiome meta-RNA-seq data. I have it a …
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I am working on calling variants in spatial transcriptomics data (10x Visium). Since the sequencing depth of spatial transcriptome is poorer than single-cell data, I want to treat all reads in the bam…
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Does NextPolish work on transcriptome assembly? If so, is there anything I should do differently with regards to running NextPolish? Thanks!
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I was wondering if it makes sense / is straight-forward to use blobtools2 to decontaminate de novo transcriptomes. If so, are there any recommendations that differ from the approaches used for genomes…
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Hello,
I have another question concerning this pipeline.
The m6A accessibility and level are calculated using in vitro samples : do you think it is possible to estimate the m6A accessibility in a…
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Hello,
We've produced in vivo probing data (SHAPE treated and untreated) to study transcriptomic structures, but shapemapper2 doesn't natively output reactivity data for entire transcriptome. We've …
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Is it a top-level fasta asset, like the genome fasta? Or, is it a child asset, with parents of a genome fasta and transcritome annotation file? then, it needs its own recipe to create the fasta asset.
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Dear team,
I'm a little bit confused about the build index step. The manual says that it builds a transcriptome index but needs as input a genomic fasta and a gff. I would like to create the count…