rna-star

Hi Alex, I'm testing how parameters impact STAR alignment and have a question about how genome

Hello Alex, I have a peculiar scenario that yields some interesting alignment results. (I'm using

Ah, thank you, that makes sense. I'll give my data another look with this in mind. Thank you! On

Hi Alexander, I work with STAR for few months. I want to study Allelic Specific Expression of rice F1

Hi Alex, The patch did not work for me. I subsetted the original fastq to one with only a few reads

Thanks Alex for the reply. What intrigues me is that, often, authors of metagenomic and

Hi Jesse, Presently there is no way to separate these classes. On Thursday, February 22, 2024 at 11:

Hi Omar, intron motifs: 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT Only 1,2 are truly

Typically, it's not worth it. You may want to check for a few samples if this is true in your

Hi Ramesh, You would need to investigate why the reads do not map - or map as multimappers when the

Hi Alex, Thank you for the clarification! Best, Josephine On Thursday, January 18, 2024 at 9:45:22 AM

Hi Sandy, You are using a very old version of STAR. Please switch to the latest one, and this will

Hi Sigal, There is nothing suspicious in the log-out file. How much RAM do you have? You would need

Hi Tonya, It looks like there was an issue with sorting. It took really long time (>7 hours).

Hi Jesse, Your description for STARsolo is correct: it performs multi-gene re-distribution for each

Hi Xiao, If chimeric alignment is not switched on, STAR does not consider it. I am not sure what

Yes, if you make a combined "genome" of two species. The cell/gene matrix will contain the

Hi Xiao, Chimeric junction detection does *not* depend on annotations, independent of whether the

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...@