User: caranlove

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caranlove0
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Posts by caranlove

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Comment: C: Counting number of hits of blastn output
... Thank you, you are correct and this worked wonderfully! ...
written 3 months ago by caranlove0
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fineRADstructure file error
... Hi all, I am working with fineradstructure for the first time and am encountering an error that I am having issues solving. I have successfully run the first command: /RADpainter paint stacks_finerad_min4.finerad This ran fine and also gave me a list of samples which have a lot of missing ...
finestructure radseq structure snp fineradstucture written 3 months ago by caranlove0
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Comment: C: Counting number of hits of blastn output
... Thank you for the insight! This is helpful, but I am actually most interested in how many of the quary sequences blasted to each of the reference/database sequences individually. Do you happen to have a suggestion on best way to get these numbers? Maybe it is best to create a custom reference file ...
written 4 months ago by caranlove0
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Comment: C: Counting number of hits of blastn output
... Thank you, yes, I am looking for some sort of summary of how many hits there were for each sequence in my database. Do you have any suggestions on how to best get counts of how many reads in my sample file blasted to each of the sequences in my blast file? Thanks! ...
written 4 months ago by caranlove0
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Counting number of hits of blastn output
... Hi all, I am working with makeblastdb and blastn for the first time and apologize for what is probably a basic question. I recently indexed and blasted against my own database, all of which are the sequences from the same species. module load BLAST+/2.9.0-foss-2018a blastn -query my.fasta ...
makeblastdb database blastn index written 4 months ago by caranlove0 • updated 4 months ago by lieven.sterck6.7k
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Comment: C: Hisat2 index builder seems to be running indefinitly
... Yes, it does appear to still be running. ...
written 5 months 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 5 months ago by caranlove0 • updated 5 months ago by ATpoint28k
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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 5 months 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 5 months ago by caranlove0 • updated 5 months ago by h.mon29k
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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 5 months ago by caranlove0 • updated 5 months ago by h.mon29k

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