User: caranlove

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caranlove0
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Posts by caranlove

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Comment: C: Hisat2 index builder seems to be running indefinitly
... Yes, it does appear to still be running. ...
written 20 days ago by caranlove0
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Hisat2 index builder seems to be running indefinitly
... Hello, I am attempting to create an new index from Emsemble reference files, and the index builder is taking far longer than what I am used to when creating a new index. The builder command has been running now for >48 hrs and I am a bit confused on why it is taking so long/if it is working. I ...
rna-seq hisat2 written 20 days ago by caranlove0 • updated 20 days ago by ATpoint22k
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Comment: C: mmquant run failure
... Thank you for the suggestion! But the job run says I am using less than 1gb and only 3-7min of the 24 hrs allotted. ...
written 24 days ago by caranlove0
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Comment: C: mmquant run failure
... Thank you for the response! The gtf file has been validated in other programs and appears to load in fine here. I allotted 4 cores and 20gb for the run as well as called -t13 as the program suggests. I am now getting the program to read in the gtf file and the bam files with: mmquant -a referen ...
written 24 days ago by caranlove0 • updated 24 days ago by h.mon27k
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mmquant run failure
... I am attempting to run mmquant and it keeps being killed after reading in the .gtf files. The script I am running is pasted below and the samples are all coordinate sorted bam files. Any ideas on why? mmquant -a Reference.gtf -r 1.bam 2.bam 3.bam 4.bam 5.bam 6.bam 7.bam 8.bam 9.bam 10.bam 18.b ...
rna-seq mmquant written 25 days ago by caranlove0 • updated 24 days ago by h.mon27k
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Comment: C: Interpreting Hisat2 alignment output
... Thank you, this is a helpful breakdown! ...
written 26 days ago by caranlove0
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Comment: C: Interpreting Hisat2 alignment output
... Thank you for the response! This is not a model organism but a closely related wild canid referenced to the CanFam3 genome. I used rcorrector and trimomatic to perform kmer filtering and remove a small amount of adapter contamination. The Illumina RNA-seq library prep was performed at a genomics co ...
written 26 days ago by caranlove0
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Interpreting Hisat2 alignment output
... I am am aligning my RNAseq data to a reference genome using Hisat2 for the first time and I have what I am sure is a basic question. However I am still confused after reading a number of online resources. Broadly, my pipeline goes from FastQC to rCorrector to Trimomatic to Hisat2, and I am not ce ...
hisat alignment rna-seq written 27 days ago by caranlove0 • updated 26 days ago by lakhujanivijay4.4k
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makeTxDbFromGFF issues and warning 6:Couldn't set synchronous mode...
... Hello, I am working with the GenomicFeatures package to create the txdb file needed for downstream analyses but am encountering a number of warnings and am unable to successfully create a txdb file. From my online searchers I have not been able to find a remedy and wonder if anyone might had advice ...
software error R rna-seq written 6 weeks ago by caranlove0
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Comment: C: BWA error when aligning multiple files
... Thank you. Do you know why this might be? Or how to move forward with this being the case? ...
written 6 months ago by caranlove0

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