rna-star

Hi Xiao, Yes, STAR chimeric detection does not use annotations, so you can chimeras between

Hi Imchen, You can generate the combined genome for all the 20 genomes, and map to it, provided that

Hi Mario, Yes, absolutely - reducing stringency at mapping and more careful post-processing is the

Hi Jurgen, When reads are mapped together, they have to map concordantly - discordant alignments are

HI Alex, Thanks for helping with STAR relating problems. I'm trying to align a read from one

Hi Alexander, For improving of STAR manual, the problem comes from a typing error : F is missing in

Hi Alex, Thanks for your reply. This still seems to get stuck at the same stage with this --

Hi Peter, STAR only looks for a complete match. On Thursday, October 12, 2023 at 3:34:39 PM UTC-4

Hi Lauren, in the 1st run, you restricted the number of mismatches to --outFilterMismatchNmax 1 with

Hi Stephen, Are you trying to map full-length transcripts? This would require STARlong, as standard

Hi Shaunak, did you use GTF file when generating the genome index? On Friday, September 8, 2023 at 7:

Hi Matt, 1) The endogenous sequence is still present, but not associated with a gtf entry. Will this

Hi Ezhil, please send me the Log.out file. On Monday, August 28, 2023 at 11:16:00 AM UTC-4 ezh...@

Hi, for "reverse"-stranded libraries, the 4th column should be used. On Friday, August 18,

Hello, I have some questions about using a genome annotation file (.gtf) as input for STAR

Hi, So I have big fastq files generated from BDRhapsody single cell sequences. To make it parallelize

Hi, a good estimate for genome size is ~(9...10)*GenomeLength, so you may need ~250GB of RAM. Another

Hi Mario, yes, these rows can be combined. Chimeric.out.junction reports the alignment of Read1 and

Hi Jack, STAR should not have a problem with rare Ns in the genome. Please check that masking Ns did

Simultaneous processes will not conflict if you use distinct --outFileNamePrefix . However, they may

Hi Laura, if you have 32GB of RAM and 8 threads, it should compete in <2 hours. And you would not

Hi Ginger, my suggestions to figure out why the alignments are "too short": 1. Map read1

Hi Stéphane STAR considers mate1 and mate2 as one paired-end read. On Friday, June 23, 2023 at 8:40:

STAR needs to know which exons belong to which transcripts, so that it can extract splice junctions

Hi, it makes sense since you used --outFilterMultimapNmax 1 This outputs only unique mappers, and all

Hi, it seems like your FASTQ file has empty sequences. If you trimmed the reads, please make sure

There is no error message here. Can you find the Log.out file that STAR generated. On Thursday, June

Hi Darwin, this is indeed strange. I would recommend adding a few sequences at a time (10100,1000...)

Hi Ellen, yes, all parameters should appear in the Log.out file. It's always a good idea to check

Hi, I would recommend using the default value (100). This parameter has typically only very marginal