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• SEQanswers – RNA Sequencing

  • RNAseq (SOLiD) from 18 - 200 nt June 18, 2013
    We are interested in small non-coding RNAs. Whomever you ask about the size range of small RNAs, you get a different answer. ;) Lets assume, small... […]
    GenomicIBK
  • Unmapped ratio very high on mouse genome June 17, 2013
    Hi, My problem regards RNA-Seq data. I've downloaded public data (SAGE libs w/ 6 different samples from mouse liver ) to analyse using ArrayStudio.... […]
    le.nono
  • RNASeq: Read length different from expected June 17, 2013
    Hello all, I have received paired-end reads for 40 samples. The reads are supposed to be 100bp per end. Instead, 20 of my samples are 101bp per... […]
    gogodidi
  • How to install xgawk June 16, 2013
    Hi, This is Shrujan, i have a problem while running RNA Sequencing QC. It shows an error that xgawk is not found. So please help me installing... […]
    shrujan
  • RNA Sequencing QC Error while using with Sequence_QC.sh file June 15, 2013
    Hi, This is Shrujan kumar Madadha, I had an error while running QC for Drosophila Yukuba fastq RNA file using Sequence_QC.sh file of FASTX... […]
    shrujan
  • Cuffmerge related query June 12, 2013
    I have a query regarding what samples should be merged using cuffmerge, when you have multiple phenotypes (each with replicates). Lets say my mouse... […]
    ParthavJailwala

• Biostar – RNA-Seq

  • edgeR: very low p-value and very high variance within the group of replicates. What's my problem??
    I'm using edgeR in order to perform differential expression analysis from RNA-seq experiment. I have 6 samples of tumor cell, same tumor and same treatment: 3 patient with good prognosis and 3 patient with bad prognosis. I want to compare the gene expression among the two groups. I ran the edgeR pakage like follow: x […]
  • Normalising tag count to RPKM
    Hi! I was wondering if their is a way to normalise the number of reads in a region and the RPKM of the nearest gene to that region, so that a correlation could be computed. Like the following data shows number of tags in first column and RPKM in second column Tags RPKM 15 0.14619 11 0 203 0.2259 129 10.701 300 7.0772 122 2.3234 346 10.666 77 3.117 201 16.749 […]
  • a simple question on RNA-Seq terminology
    This question may be very simple and basic, but I just need to confirm that I understand the differences among those terminologies in the RNA-Seq context. Suppose I have a sample called SLR, and it is sequenced on 5 lanes, so I have (among other output files) BAM files like L1_SLR, L2_SLR, L3_SLR, L5_SLR and L7_SLR.bam. Here, the letter "L" denotes […]
  • FInding regions of interest with minimum coverage
    Hi, I have a bam file of all my accepted hits (tophat output) and an gtf file with my genes of interest for which I am trying to find potential antisense transcripts. I would like to create a list - preferably one that can be visualized in a genome browser - that shows all genes that have antisense reads in the accepted hits.bam file provided that there are […]
  • How to remove the intronic reads before counting
    I got RNASeq data in several samples. I checked the FastQC, seems the read quality are good (Hiseq 2000). But the problem is many reads are mapped to intronic region, and the regions have no any reference exons there (Refseq, ensembl, gencode). We don't know what they are. We guess the problem happend in library preparation, the concentration was low. N […]
  • Which strand of the mRNA molecule does the sequencer output as a "read"?
    In Illumina Stranded RNA-Seq (using the dUTP method), do the final reads in the fastq files correspond to the initial molecule (that was transcribed), or to the reverse complement of the molecule? C […]