Hi,
I used STARsolo but my bam files, below, are missing barcode and UMI info:
```
(/scratch/work/malonzm1/.conda_envs/scvi-env)...
38 results in 0.0023 seconds.
-
bam file missing barcode and UMI info
-
STAR ERROR: not enough memory for BAM sorting
Dear all,
I am struggling to get this command right, and getting errors all the time.
First Error:
$ STAR --genomeDir... -
Non-ascii characters in bam file causes htseq-count error
Hello everybody,
I have aligned bam files (using STAR version 2.6.1a_08-27) and want to quantify them using htseq-count (version 0.9.1).... -
Non-ascii characters in bam file causes htseq-count error
Hello everybody,
I have aligned bam files (STAR version 2.6.1a_08-27) and want to quantify them using htseq-count (version 0.9.1). When... -
cufflinks does not understand strands?
Dear All,
I used STAR to map paired-end reads onto the reference genome:
...Code:~/apps/STAR/bin/Linux_x86_64/STAR --runMode
-
Handling pseudogenes in RNA-seq
I recently performed an RNA-seq experiment that was mapped using STAR through a package called zUMIs. Typically, our reads are 66 bp (and in the past... -
Remapping reads
hello!
Currently I am working with a large set of STAR mapped reads, the output is in sam format. I would like to remap, but was wondering if its... -
RNA-seq read alignment best practices for low-input Smart-seq2 samples
RNA-seq read alignment best practices for low-input Smart-seq2 samples
Hi All,
I think my data may fall in a nether region between... -
Align full length contigs instead of reads
Hello,
Splice aligners like HiSAT2 and STAR are optimised to map short reads (~100bp) to large genomes. I have assembled contigs available.... -
RNA-seq alignment on novel region
Hi everyone,
My colleagues just discovered a novel lncRNA region and I would like to check its expression in my 30 RNA-seq samples. The length... -
Quality trimming prior to aligning
I am aligning reads to the GrCh37 human reference genome using STAR and am confused as to how to get the most reliable results. At first I aligned my...Last edited by gstone; 02-28-2017, 03:48 PM. -
Anybody proficient with Hamilton/Venus?
Hi all, I hope this isn't a long shot or inappropriate for this forum...
I'm having troubles with a script I've written for a Hamilton... -
STAR - Analyzing RNAseq data from degraded RNA for both, mRNA and miRNAs
Hi,
I am using STAR to align my RNAseq reads and I realize that the parameters for looking for miRNAs (or other short RNAs) are very different... -
Weird output STAR mapping R1 and R2 separately vs combined
Hi,
I am just starting to learn using STAR for RNA-seq mapping. I made libraries from low-input, degraded (and likely enriched in short... -
STAR aligner - Segmentation fault (core dumped) multiple fastq paired-end samples
Hi,
I am using STAR-2.5.2b on virtualbox with 65 gb of RAM assigned and 28 CPUs/threads.
When I ran STAR with single paired-end sample,...
