User: devbt15

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devbt1530
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Posts by devbt15

<prev • 7 results • page 1 of 1 • next >
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Source fasta sequence options unavailable
... Dear all, While trying to use the data manager for hisat2 index building, I do not get any dropdown options for the source fasta sequence, although I have uploaded the genome.fasta file to my data on local galaxy. I also tried the NormalizeFasta command from picard tool on the genome.fasta file but ...
data manager manager local data hisat2 index written 23 days ago by devbt1530 • updated 20 days ago by Jennifer Hillman Jackson23k
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Error: You must set the environmental variable TRINITY_BASE_DIR to the base installation directory of Trinity before running this
... Dear all, While using trinityrnaseq_protocol, I have encountered the error (as described in the title of the question). I am running local galaxy from the bash terminal for Ubuntu on my windows PC. Please help. Unfortunately, this question was raised on Biostars but has not been answered yet: https ...
local galaxy rna-seq trinity written 27 days ago by devbt1530
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Answer: A: Annotation file formats .gff3 to .gtf conversion
... Dear Jen, I have shared a new history folder with the concerned .gff3 file in it and shared it so it is accessible to all as I could not send it to galaxy-bugs@lists.galaxyproject.org. Meanwhile in my workflow, for Salmon, I used the .gtf file (position information, IDs, feature type etc.) convert ...
written 4 months ago by devbt1530
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Annotation file formats .gff3 to .gtf conversion
... Dear all, I used the Galaxy tool to convert the .gff3 annotation file to .gtf format. Going through the .gtf file, I discovered few entries where transcript ID is present but no corresponding gene ID or gene name is available. I am getting an error when running DESeq2 analysis using this .gtf anno ...
galaxy rna-seq written 4 months ago by devbt1530
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Answer: A: salmon gene quant to DESeq2
... **Dear all, I used the same pipeline and used the SALMON output for DESeq2 (there is an option of TPM input) along with .gtf of annotations. It gave me an error eventually:** Fatal error: An undefined error occurred, please check your input carefully and contact your administrator. Warning messages ...
written 4 months ago by devbt1530
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Answer: A: Insert sizes in Galaxy
... Dear Jen, Thank you for responding to my query. I have already gone through answers to similar questions posted on Biostar. 1) And also tried it on my dataset which was from DRA dataset Japan. It mentioned the nominal length as 300 which in their database tutorial is termed equivalent to insert si ...
written 4 months ago by devbt1530
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Insert sizes in Galaxy
... I am new to RNASeq analysis. I used tophat to generate BAM files from FASTQ files but in the parameter options set "Mean Inner Distance between Mate Pairs" to 150 assuming insert size to be around 300-400 and the read lengths were 100. Eventually, I input the BAM file to "CollectInsertSizeMetrics" f ...
galaxy bowtie tophat rna-seq written 4 months ago by devbt1530

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