User: tkirkland

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tkirkland0
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Posts by tkirkland

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Trying to Assemble SRAs with Unicycler
... I'm trying to assemble SRA reads from NCBI and I'm getting the error "Remote job server indicated a problem running or monitoring this job. display with IGV local 5 Create assemblies with Unicycler on data 4: Final Assembly Graph tool error An error occurred with this dataset: ...
unicycler assembly written 7 days ago by tkirkland0
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Covert fast.gz files to fastq
... I am trying to run this conversion and it just won't run. It has been gray for more than 3 hours. Am I doing something wrong? The name of the history is C_immitis_posadasii_sph ...
rna-seq written 6 months ago by tkirkland0 • updated 6 months ago by Martin Čech ♦♦ 4.8k
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Salmon unique reads
... I have found Salmon a very good tool to run a set of RNA-seq reads against a fasta file and get meaningful results. However, I would like to get unique hits. Is the default output unique or not? If not, is there a way to change the settings to get unuiqe reads? ...
read unique salmon rna-seq count written 6 months ago by tkirkland0 • updated 6 months ago by Jennifer Hillman Jackson25k
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Over disk quota
... I keep going over disk quota. I am trying to analyze RNAseq data from a total of 6 SRA files - that doesn't seem right. Also - I can't figure out how to log out to reset anything. What am I doing wrong? ...
quota reset account purge delete written 8 months ago by tkirkland0 • updated 8 months ago by Jennifer Hillman Jackson25k
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Fastq files not recognized
... I have uploaded data sets that are labelled fastqsanger.gz. But when I try to use those data sets I get the message "No fastqsanger.gz data set available". Can you tell me what I am doing wrong? Thanks Theo ...
fastqsanger input tools fastqsanger.gz fastq written 8 months ago by tkirkland0 • updated 8 months ago by Jennifer Hillman Jackson25k
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bwa not recognizing fastq files
... I am trying to map a set of fastq sequences to a custom genome, using BWA. The two setrs of triplicates are in a collection and I have run groomer on them. to convert to fastqsanger. When I try to run BWA (or BWA-mem), I get the error "No set or collection of fastqsanger availabl". Olease help ...
rna-seq written 14 months ago by tkirkland0
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Lading SRA files into Galaxy
... I have been trying to load SRA files into Galaxy. I have tried using SRA tools, EBI download and FTP from my computer. None of these work. Do you have any idea what I'm doing wrong? Thanks Theo ...
rna-seq written 14 months ago by tkirkland0 • updated 14 months ago by Jennifer Hillman Jackson25k
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Problem with Tophat
... I'm trying follow the steps of the example from the Galaxy Training on RNAseq. After loading the data and putting it into folders I started Tophat as instructed. The error message that I got for accepted hits was "An error occurred setting the metadata for this dataset Set it manually or retry aut ...
rna-seq written 15 months ago by tkirkland0 • updated 15 months ago by Jennifer Hillman Jackson25k
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(Closed) Cufflinks stuck analyzing HISAT data
... Hi Jen, I have processed my data with HISAT and gotten several cufflinks jobs to run. However, I have a total of 6 HISAT data sets that I need gene tables for and haven't been able to get cufflinks to run since Thursday (5/11). Do you have any ideas? Thanks Theo ...
rna-seq written 15 months ago by tkirkland0
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time to run cufflinks
... How long does it take to run cufflinks? It has been submitted for 48 hours and still has the gray color with the !. ...
rna-seq written 15 months ago by tkirkland0 • updated 15 months ago by Jennifer Hillman Jackson25k

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