38 results in 0.0025 seconds.
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STAR alignment - splice acceptor site vs mismatch
This is more a question about how STAR works. In figure 1 of the paper (here), the aligner can either look for a splice acceptor site or extend beyond... -
Should discordant pairs be used for counting/DGE?
Hello everyone,
I am using the STAR aligner, which reports discordant pair alignments in a seperate BAM file. Using my workflow I want... -
STAR Alignment parameters for varying complexity in library
I'm working with TruSeq data for the mouse genome, with one of the groups having a low complexity library, and the other two having a high complexity... -
Looking for advice on generating a transcriptome from mapped .bam or .sam files
Hello all. I'm starting off here with something fairly complex, I guess.
I'm looking for some advice because I'm starting a new project... -
Convert .fna file from NCBI to .fa or .fasta file
Hello,
I am totally new to this (I am a student following a course in bio-informatics) and I wanted to use a genome found on NCBI (in .fna or genbank... -
RNA-Seq strandedness inconsistency
Hi,
Let me start of by saying that I am thoroughly confused and I hope someone can help me make sense of my data.
I have...Last edited by Anomilie; 11-20-2015, 01:41 AM. -
RNA STAR does not seem to work for microbial/small genomes
Hi everyone,
I am having some trouble with creating genome indexes with STAR. I double checked the manual and I am using all the correct... -
How to get FPKM values for Ensembl
Hello Everyone,
I am scratching my head because I just can't seem to find a way to calculate FPKM values for Ensembl genes. I aligned the... -
mmseq gzip error
I'm running mmseq to calculate expression from STAR (2-pass) alignments. Mmseq completes just fine, no errors in stderr/stdout. But, it seems that the... -
STAR segmentation fault (--genomeSAindexNbases not reassigning?)
Hello!
I have used STAR successfully in the past to align with large reference genomes. I am now trying to align with a small genome (~3230... -
RNA-Star : SJ.out.tab differents according to 'outFilterType' value?? and
Hello,
we are using RNA-Star to our project (thank to authors!).
I don't understand a difference observed about the SJ.out.tab files... -
using STAR+Cufflinks for transcript assembly turns unstranded RNA-seq to stranded?
I am trying to use STAR+Cufflinks to do a reference based transcript assembly using unstranded RNA-seq data.
As mentioned in the STAR... -
Reassign mapping quality in STAR / GATK/ Cufflinks compatibility
Hello all,
I'm reassigning mapping quality values produced by STAR from 255 to 60 (column 5 of the output) for GATK compatibility and I... -
Can I use preproccesed bam files for Cufflinks?
This question has been asked here previously: http://seqanswers.com/forums/showthr...s+preprocessed
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STAR + Cufflinks. Cufflinks hanging. BAM XS error?
Hello All,
I have an RNA-Seq pipeline, using the STAR aligner and Cufflinks.
I am running cufflinks in the 'Reference Annotation...
