rna-star

Hello, I am comparing the duplication rates of the transcriptome-aligned vs genome-aligned bams using

Great! Thank you!! On Wednesday, September 8, 2021 at 2:37:57 PM UTC-7 ado...@gmail.com wrote: Hi

Hi Alex, Is there a reason why non-canonical splice sites should be removed for running the second

Thank you :) On Wednesday, 8 September 2021 at 22:33:18 UTC+1 ado...@gmail.com wrote: Hi Bekah, you

Hi Eleni, if the mitochondrial chromosome and genes are present in the genome FASTA and GTF files,

Hi Sophie, generally, mapping to the combined genome of all species is the most straightforward

Dear all, I am relatively new to the field and I am trying to use STAR to do alignment and count in

Hi Adi, STAR cannot be run on Windows, unfortunately. In principle, you can try to do it with cygwin,

Dear Alex, I am currently working on Smartseq2 data and was thinking about what to choose for --

Hi Dario, thanks for the suggestion, I will add the description of this option into the manual.

Hi, this means that zlib library is missing, you would need to install it before compiling. Cheers

Hi Zhijie, it can happen with some parameter settings - what parameters are you using? Note that for

Hi Mazlina, this warning means the Log.out file could not be moved to the genome directory. What was

Hi Jason, since you are adding a very large number of junction (~7M), you would need to do it at the

Hi Konstantin, this feature is not available yet, unfortunately. I am getting a number of requests

Hi Alessa, presently, there is no tag on STAR SAM output to indicate which gene the alignment belongs

Hi Dongmeng, If you run --twoPassMode Basic, WASP filtering is not done at all in the 1st pass. The

Hi Gray, quantification does not change BAM ot other outputs. Cheers Alex On Sunday, May 9, 2021 at

Hi Marianne, the GTF looks good, but you need to specify it with --sjdbGTFfile ann.gtf at the genome

Hi Julia, --varVCFfile does not incorporate the variants into the genome. Is the cell line is from

Hello Alex, Thanks for your instruction. I went back to check, and it's 1.10, which was released

https://github.com/alexdobin/STAR/issues/1209 On Monday, April 26, 2021 at 4:57:52 PM UTC-4 fumiaki

Hi Alex, I apologize for my late response - thank you for the informative reply! Sincerely, Anna On

Hi @yuquantong97 This is probably normal - it means that only ~26% of your reads are miRNA. The rest

Hi Lluc, shorter reads will map to more loci in the genome (check the Log.final.out file), and even

Hi Oladele, 1. You would need to run a loop over your files, changing the --outFileNamePrefix for

Hi Alex, I've been trying to use the .bam files obtained with STAR in RSEM, but I am having some

Hi Yoyo, If the reads have exactly the same sequences, they should map to exactly the same loci. The

Hi Maria, this means that there is micro-repeat around the junctions, which mean the donor and

Hi Kevin, presently this is not possible. This had been long on my TODO list... I might have time to