Ignore the typo in the title please...
I've been struggling to understand this plot. At first glance I thought it was telling me how many...
22 results in 0.0030 seconds.
-
What does teh 51-mer count distribution plot in Preqc Output represent?
-
intersect file bam-bed and count read
Hi all!
I have RNA-seq data and I used STAR in order to align the reads.
I would like to use my bed file in order to have the only read... -
Assigning reads to genes in the absence of genomic annotation
I'm looking for a method to calculate read counts from SAM/BAM files that does not require an annotation file (GTF or BED files).
I've... -
Annotate gene list
I would like to annotate the results output file from Desq2 so it contains gene names and symbols. The RNA-seq count file I have used comes from Dexseq... -
Counting the total number of SNPs in a transcript
Hi,
I have RNAseq data that has been aligned to reference transcriptome and the aligned bam file is sorted and indexed.
... -
Count BLAST hits and 'no hits'
I'm performing local blastn.
My query file consists in 20 sequences, and I have my own databases (DB) created out of several short reads Illumina... -
Error in htseq-count. Large gaps in CIGAR string
Hi,
I am getting this error when I run htseq-count (version 0.5.4p3)
Error occured in line 6684695 of file OUT.gsnap.combined.Control_72_Rep3_R1.fastq.uniq.... -
Count reads around breakpoint (rna-seq)
Hej there,
I'm trying to detect gene fusion with rna-seq. The draft below is showing
an example of how reads spanning read and split...Last edited by spoonman; 07-29-2014, 08:49 AM. -
HTSeq exon counts to gene level
Hi,
I'm working with drosophila melanogaster RNA-Seq data and at least one of my genes of interest is overlapping an other gene so I used... -
Creating a gtf file for the database I mapped against
I used BWA-SOLiD from Galaxy, but had somewhat of a mapping failure with very little hits. It was kindly suggested to me by Jennifer of Galaxy:
... -
No reads mapped using BWA SOLiD
I am trying to troubleshoot why no reads were mapped in my call to BWA SoLiD in Galaxy. I also posted about this on Biostar here (https://biostar.use... -
Online tools to generate count tables from sam/bam files
Does Galaxy or any other online tools offer methods to generate a count table from bam or sam files? -
filtering - find-if commands
Hi, Could someone please tell me how to do this simple search. I don't know much programming and this is beyond me. But I think it should be a simple... -
Python counting bases fasta file
New to python but trying to learn, here I wrote a program to count the nucleotides in a fasta file. The approach is that when the line does not contain... -
Align reads to 1 gene
Hi All,
I need to align ABI Solid reads to just 1 gene to see how many reads align to just that gene. (No mapping has been done so far)....
