User: devikaparvathy

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Posts by devikaparvathy

<prev • 9 results • page 1 of 1 • next >
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Convert genome coordinates between assemblies and genomes (Galaxy Version 1.0.5) aka LiftOver
... I have two related bacterial genomes of same species - different subspecies. I want to map the co-ordinates of one genome to the other. How do I use the Liftover tool in galaxy for this? What format of the target organism genome is required? Note: I have the gff file and FASTA files of both the sou ...
liftover convert genome co-ordinates ucsc written 3 months ago by devikaparvathy10 • updated 3 months ago by Jennifer Hillman Jackson23k
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Error in DESEQ2
... I am obtaining the following error while working with DE-seq2: Fatal error: An undefined error occured, please check your intput carefully and contact your administrator. Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' Error in parse(text = x, keep ...
known-issue deseq2 usegalaxy.org tool error written 14 months ago by devikaparvathy10 • updated 14 months ago by Jennifer Hillman Jackson23k
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Comment: C: Differential Expression of bacterial non-coding sRNA
... Is it advisable to use different methods of expression analysis for the mRNA's and sRNA's if i want to compare them and extract oppositely regulated pairs? ...
written 14 months ago by devikaparvathy10
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Answer: A: CUFFDIFF in Galaxy not working for past few days
... Hi thanks. I have mailed with all necessary details to the galaxy bugs list. ...
written 14 months ago by devikaparvathy10
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Answer: A: CUFFDIFF in Galaxy not working for past few days
... Tried that too and also tried logging in and out many times. Usually once the task is submitted, the main page itself lists out the numbers and list of new datasets that will be generated. Here I am not even getting that. Is there anyway I could share my activity/ page to show you what's happening? ...
written 14 months ago by devikaparvathy10
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Answer: A: CUFFDIFF in Galaxy not working for past few days
... Hello, Thank you for the reply. But the issue seems slightly different in that, the jobs are not even being added (No new datasets added to the history pane) Only the following message is shown - (but there is no list of the new datasets that is usually shown alongwith) "1 job has been successfu ...
written 14 months ago by devikaparvathy10
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CUFFDIFF in Galaxy not working for past few days
... I have been using Galaxy webserver at usegalaxy.org for my works, and suddenly for the past few days I am unable to run CUFFDIFF successfully. The input pages are coming correctly, but no output files are created. I have used CUFFDIFF in galaxy previously and this is the first time I am encounterin ...
cuffdiff usegalaxy.org job queue tool written 14 months ago by devikaparvathy10 • updated 14 months ago by Mo Heydarian790
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Answer: A: Differential Expression of bacterial non-coding sRNA
... Thank you for your detailed answer. Infact I am doing non-coding RNA's in bacteria, and currently focus only on the differential expression and not on identification of novel sRNA's (That part was done earlier by another team and I am using their annotation for my works). ...
written 15 months ago by devikaparvathy10
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Differential Expression of bacterial non-coding sRNA
... I am analysing both sRNA data and mRNA data for differential expression from bacteria. For mRNA-seq I used the pipeline Bowtie+Stringtie+Ballgown. For sRNA i am planning to use, Bowtie+HTseq-count+DESeq2. I opted for HTseq2 + DEseq2 as I didnt find any previous references that have used STRINGTIE fo ...
srna-seq htseq rna-seq deseq2 stringtie written 15 months ago by devikaparvathy10 • updated 15 months ago by y.hoogstrate450

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