• Read count per exon per transcript

    Hi

    How can I get a read count per exon per transcript in a particular gene from BAM file? I trie...

  • Salmon quantification vs HTSeq count quantification

    Hi guys,

    I've got a question. Can we compare the quantification files from Salmon and from HTseq...

  • HTSeq-count no feature is too high

    Hello,

    I'm using HTSeq-count to determine the number of transcripts for each sample. I have bam ...

  • Read Counts From Sam File Mapped To De Novo Assembled Transcripts Using Htseq-Count

    Hello,

    I tried using HTSeq-count to extract read counts per transcript from the SAM file (genera...

  • htseq counts on genes (introns + exons)

    Hello,

    I was wondering if there was a way of using htseq to count the number of reads per genes...

  • Difference between HTSeq-count & Salmon quant results

    Hi guys,

    I've already posted a question about Salmon earlier , but this one is totally different...

  • Where Do I Get A Gtf File With Proper Gene Ids For Read Counting?

    I've just noticed that the knownGene.gtf file that you can download from the UCSC browser (for e....

  • Plot transcripts with exaggerated exons and very short introns in R

    I have to visualize a transcript and reads that align to it. The problem is that the transcript h...

  • counting reads for genes

    Hello, I am counting number of reads assigned to each transcript using htseq-count after aligning...

  • merge PE reads for Transcript De-Novo Assembly ??

    Dear all,

    Do you recommend merging pair-end Illumina reads for Transcript De-Novo assembly?  Tha...

  • What Is A "Gene"? Redundancies In Refseq Versus Ensembl

    Whenever I annotate microarray probes or RNASeq reads and want to have information at the gene le...

  • Sequencing Strandedness and Differences in Expression Readouts Between stringtie and htseq

    I am rather new to RNAseq, particularly when it comes to processing my own data. Please excuse an...

  • Rpkm Calculation For Genes

    Hi everyone

    I understand the RPKM fomula is as follows:

    C = Number of reads mapped to a gene

    N...

  • HTSeq-count in RNA-Seq

    **strong text**hello everybody,

    I'm doing for the first time an analysis of differential gene ex...



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