groHMM input data

I am attempting to use the groHMM package from Bioconductor to preform a metagene analysis.

I've played around with the included sample data and was able to get most of the tutorial done. However, attempting to use my own input files have proven ... errr ... well it's gone badly.

I had assumed that the input data prior to wiggle creation was bam files as specified in the vignette, but my bam file (13gb) causes an error when attempting to read in that file via Rsamtools because it's huge file size. So i'm wondering if this file type is even the correct input.

Hoping someone could help me out.

Thanks.

r grohmm

• 1,478 views • link

written 10.6 years ago by dally

0 answers

No answers yet.

More posts like this

SRAtoolkit error during fastq-dump
written 10.5 years ago by dally

I downloaded an SRA file from GEO FTP. I then ran the following command trying to grab the fastq files, but I keep coming up …
Split BAM file into two subsamples
written 10.5 years ago by colin.kern

I want to create two random subsamples from a BAM file. I don't want to just do "samtools view -s 0.5" twice because I want …
Individual colors for heatmaps using ngsplot
written 10.6 years ago by dally

I am using NGSPLOT to generate heatmaps of a couple of TF's, but the output only gives me the same color for each heatmap. I …
Stuck creating reference genome with STAR
written 10.6 years ago by nash.claire

Hi again, I want to use STAR to run my RNA-seq analysis however I'm having issues at the first hurdle trying to generate a reference …
Converting .narrowPeak file to GRanges for use in Bioconductor ChIPseeker
written 10.8 years ago by dally

I have a .narrowPeak file of Pol IIthat has called peaks using MACS2 and has annotated the peaks using HOMER. I am attempting to visualize …
Extracting counts from RNA-Seq: trouble with bedtools + multicov
written 10.9 years ago by Kristin Muench

Hello, I just aligned my first piece of RNA-Seq data and have a .bam file. I'd like to make a file of counts corresponding to …
convert2annovar Skipped invalid alternative alleles found in input file
written 11.3 years ago by giovannadv •

Hi, I' m a new user; I've tried to convert my vcf4 file withconvert2annovar file to obtain a input file to analize with ANNOVAR. I' …
BAM format file to FASTA alignment file
written 11.5 years ago by ben.ward •

Hi, I've been given a reference genome and BAM file(s) which are reads aligned to that reference. This will be the first time I've done …
Extract reads with variant at given position
written 11.5 years ago by philip.jonsson •

I want to be able to extract, from BAM files, the reads that, for a given position, contain the variant (and conversely but separately, the …
Extracting a trimmed output from a bam file
written 12.2 years ago by Will

I'm tying to extract a specific region of a bam-file into a fasta-file (ultimately). All of the methods I've tried so far give me all …