User: h.stotz

gravatar for h.stotz
h.stotz20
Reputation:
20
Status:
New User
Location:
European Union
Last seen:
3 weeks, 4 days ago
Joined:
2 years, 10 months ago
Email:
h******@herts.ac.uk

Posts by h.stotz

<prev • 20 results • page 1 of 2 • next >
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Problems with understanding cufflinks output
... Good evening, I did Cufflinks correspnding to an annotated genome. I want to download transcripts to a specific gene. This particular gene has a transcript_id that corresponds to the gene of the annotated genome, but there is not "CUFF.#" for the gene_id. Nevertheless, there is FPKM information. ...
cuffdiff gene cufflinks transcript rna-seq written 25 days ago by h.stotz20 • updated 25 days ago by Jennifer Hillman Jackson25k
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Transcript sequence from Cufflink information
... Good evening I have successfully used TopHat and Cufflinks. I have selected a single annotated gene and I do have the FPKM information for it. However, I do want to compare the assembled transcript sequence to the reference gene sequence. How can I obtain this sequence? Kind regards, Henrik ...
rna-seq written 29 days ago by h.stotz20
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Get Data > ENA SRA - slow or failed downloads try NCBI instead
... Dear Jen, This is becoming quite frustrating. When I use your tool Get Data > ENA SRA it just connects me to the following website: https://www.ebi.ac.uk/ena/data/search?GALAXY_URL=https%3A//usegalaxy.org/tool_runner%3Ftool_id%3Debi_sra_main I then go to: https://www.ebi.ac.uk/ena/data/view/S ...
fastq ena-sra galaxy ncbi get-data written 5 weeks ago by h.stotz20 • updated 4 weeks ago by Jennifer Hillman Jackson25k
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Decompression of sra files and further analysis
... Case: 05508803 Dear Jen, Thanks that you are trying to help me. How can I uncompress the three sra files I have downloaded? I want to do Tophat and Cufflinks on the sra files to find out the transcripts that correspond to a specific gene BnaA07g22940D in a published genome. I do use https://us ...
srr fastqsanger rna-seq sra fastq written 5 weeks ago by h.stotz20 • updated 5 weeks ago by Jennifer Hillman Jackson25k
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Unable to view data of converted srr file into sra format
... Good afternoon, I downloaded an RNAseq file in .srr format using ftp in Galaxy. The file was converted into sra format. However, I cannot view the data. When I try to view the data, it gives me an option to open the file or to save the file. I do not know how I can utilise the file in Galaxy. T ...
srr sra rna-seq written 5 weeks ago by h.stotz20 • updated 5 weeks ago by Jennifer Hillman Jackson25k
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Downloaded .ssr file cannot be opened in Galaxy
... Good afternoon, I successfully accessed a public RNAseq dataset as an .srr file into Galaxy. However, I cannot open this file and now I am downloading the .sra file on my local computer to upload it again into Galaxy. There must be an easier way. Kind regards, Henrik ...
srr sra rna-seq upload get-data written 5 weeks ago by h.stotz20 • updated 5 weeks ago by Jennifer Hillman Jackson25k
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Inability to upload SRR file from website
... I am trying to upload SRA or SRR files from ENA, but Galaxy fails and my files are red. The info says "The uploaded file contains invalid HTML content". Can you help me with this? For instance, I like to upload SRR3134040. Many thanks, Henrik ...
srr galaxy ebi-sra sra get-data written 6 weeks ago by h.stotz20 • updated 6 weeks ago by Jennifer Hillman Jackson25k
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Trouble with joining two datasets
... I am trying to join two datasets. Each of the datasets has a row that explains column entries. However, when the two datasets are joined this row gets deleted. This is the first time I am experiencing this. I am not sure how I can solve this problem. Thanks, Henrik ...
galaxy written 15 months ago by h.stotz20 • updated 14 months ago by Jennifer Hillman Jackson25k
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Tophat job running for two days
... Hello, My Tophat job has been running for two days not. In the meantime I just completed an auto-detect job in less than an hour. Is it possible that the Tophat job was started when there was a server problem and does not get through? It is yellow. So, it may just be in a queue and eventually f ...
rna-seq written 17 months ago by h.stotz20 • updated 17 months ago by Jennifer Hillman Jackson25k
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Problems with Tophat
... Hello, I submitted a Tophat job recently and received the following error: An error occurred setting the metadata for this dataset Set it manually or retry auto-detection The files looked o.k. though. I started another Tophat job yesterday but it did not complete yet. I will keep trying. Shoul ...
rna-seq written 17 months ago by h.stotz20 • updated 17 months ago by Jennifer Hillman Jackson25k

Latest awards to h.stotz

Popular Question 29 days ago, created a question with more than 1,000 views. For Enrichment analysis and Fisher's exact test
Popular Question 15 months ago, created a question with more than 1,000 views. For Extract chromosome sequences from genome fasta file

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