User: matthew.nicotra

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Posts by matthew.nicotra

<prev • 5 results • page 1 of 1 • next >
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Comment: A: HISAT seems to assign wrong XS tag value to some reads of stranded RNAseq data
... Upon further investigation, it seems like HISAT2 is being run with the --rna-strandness parameter set to R and not RF, despite the fact that we selected paired end reads. Here's the information from Galaxy for the HISAT run: HISAT2 Dataset Information Number: 1 Name: HISAT ...
written 25 days ago by matthew.nicotra10
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Answer: A: FTP file problem connexion
... Hi Anna, Are you following the instructions for Filezilla in the video here: https://galaxyproject.org/ftp-upload/ The video seems to have the most up to date instructions on how to connect. Matt ...
written 26 days ago by matthew.nicotra10
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Answer: A: HISAT seems to assign wrong XS tag value to some reads of stranded RNAseq data
... Hi Jen, We still seem to be having trouble. We've tried setting the HISAT2 option to report alignments for Cufflinks, Stringtie, and "default". In all cases the reads with a 147 get an XS:A:+ instead of XS:A:- Is there another setting we are missing? Thanks, Matt ...
written 26 days ago by matthew.nicotra10
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Comment: A: can't access usegalaxy.org
... I was having the same issue with all browsers on both a desktop PC and a laptop mac. I seem to have fixed the problem on my Mac in Chrome by clearing the cache and app data (shift-command-delete to open the dialog) But clearing the cache on my PC doesn't help. All I get is a black line across the ...
written 27 days ago by matthew.nicotra10
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HISAT seems to assign wrong XS tag value to some reads of stranded RNAseq data
... Hi All, I have some paired end stranded RNAseq data prepared using an Illumina TruSeq Stranded mRNA kit. I have mapped the reads to the genome using HISAT. Based on my understanding of the SAM flags, concordant reads should be assigned XS values as follows: If gene is on the forward strand of the ...
rna-seq software error hisat written 27 days ago by matthew.nicotra10

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