User: tran_tim

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tran_tim10
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Posts by tran_tim

<prev • 10 results • page 1 of 1 • next >
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Cutadapt need adaptor sequence input
... I use cutadapt on galaxy to trim my adaptors for my fastq files. Does the program find a default adapter or do I have to enter in the sequence of my adapters I want to trim. I am getting this output without entering any known adaptors. This is cutadapt 1.11 with Python 2.6.6 Command line paramete ...
trimming qa fastq adaptors cutadapt written 15 months ago by tran_tim10 • updated 15 months ago by Jennifer Hillman Jackson23k
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Installing tools from Tool shed into galaxy - Public versus private instances
... I am using a public instance of Galaxy. I need to install a new tool from the Tool Shed into this same galaxy instance. Does anyone know how to do this? I went to the Tool Shed and click on the Tool but how do you get it into my galaxy instance? ...
usegalaxy.org local install admin tool written 15 months ago by tran_tim10 • updated 15 months ago by Jennifer Hillman Jackson23k
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Comment: A: htseq count problem
... chr1 havana gene 11869 14409 . + . "gene_id ""ENSG00000223972""; gene_version ""5""; gene_name ""DDX11L1""; gene_source ""havana""; gene_biotype ""transcribed_unprocessed_pseudogene""; havana_gene ""OTTHUMG00000000961""; havana_gene_version ""2"";" Above is the the 6th line of the file. ...
written 15 months ago by tran_tim10
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Reference annotation GFT GFF3 problem with tool HISAT
... I got the following error while running htseq count: I think it is my gtf file problem. How to fix it? Fatal error: Unknown error occured Error occured when processing GFF file (line 6 of file /galaxy-repl/main/files/017/359/dataset_17359504.dat): The attribute string seems to contain mismatched ...
input gtf gff3 format hisat written 15 months ago by tran_tim10 • updated 15 months ago by Jennifer Hillman Jackson23k
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Comment: A: Tophat run not working on run
... I got the following error above after running Tophat on a Fastq files.What is wrong? ...
written 15 months ago by tran_tim10
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Failed job "Tophat"
... Fatal error: Tool execution failed [2016-09-27 02:31:32] Beginning TopHat run (v2.1.0) ----------------------------------------------- [2016-09-27 02:31:32] Checking for Bowtie Bowtie version: 2.2.5.0 [2016-09-27 02:31:32] Checking for Bowtie index files (genome).. [2016-09-27 02:31:32] Checki ...
usegalaxy.org cluster tophat tool error written 15 months ago by tran_tim10 • updated 15 months ago by Jennifer Hillman Jackson23k
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Bedtools coverage not accepting file b
... Bedtools coverage does not accept the -b files. Compute both the depth and breadth of coverage of features in file A across the features in file B (coverageBed) . I can chose file A the bed files , but not file B which is my Bam files. What is wrong? Tim ...
bam written 16 months ago by tran_tim10 • updated 15 months ago by Bjoern Gruening4.8k
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Tool error "IOError: [Errno 2] No such file or directory"
... I receive the following error while running tophat: Traceback (most recent call last): File "/galaxy-repl/main/jobdir/013/902/13902630/set_metadata_GiK6KF.py", line 1, in from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy_ ...
usegalaxy.org job tophat tool error written 16 months ago by tran_tim10 • updated 16 months ago by Jennifer Hillman Jackson23k
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Answer: A: TopHat not working
... I receive the following error while running tophat: Traceback (most recent call last): File "/galaxy-repl/main/jobdir/013/902/13902630/set_metadata_GiK6KF.py", line 1, in from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/cvmfs/main.galaxyproject.org/galaxy/lib ...
written 16 months ago by tran_tim10
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TopHat not working
... My tophat in galaxy is not working. I try to use it to map to the reference human hg19 genome. But the run failed because there is a red mark check on each datasets from the examples. ...
tophat written 21 months ago by tran_tim10

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