User: scholtz

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scholtz60
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Hungary
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Joined:
2 years, 2 months ago
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Posts by scholtz

<prev • 12 results • page 1 of 2 • next >
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Stringtie Deseq2/EdgeR count tables all zero
... Dear Galaxy Team, I encountered a different problem with Stringtie + output additional files for DESeq2/EdgeR. Running the external GTF dataset (hg19 reference) through Stringtie Merge indeed makes it acceptable for Stringtie + output...etc., but the count tables are are all zero for every transcr ...
hisat2 stringtie rna-seq deseq2 written 6 days ago by scholtz60 • updated 6 days ago by Jennifer Hillman Jackson23k
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Comment: C: Purge deleted datasets not working
... Thanky you very much, looks like it's fixed now. Regards, Beata ...
written 9 months ago by scholtz60
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Purge deleted datasets not working
... Dear Galaxy Team, The "Purge deleted datasets" is not working, and I cannot remove the datasets with the "Permanently delete" command either. Hasn't improved after trying to initiate it several times, also no change after logout/login. All other functions are working fine. Your help would be gre ...
purge or permanently delete datasets written 9 months ago by scholtz60 • updated 9 months ago by Jennifer Hillman Jackson23k
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Answer: A: Separating (F and R) reads uploaded from NCBI SRA & mapping them using BWA-MEM
... This is what I've been using, following the suggestion of the Galaxy team - you will end up with separate forward/reverse data files: 1. Upload the SRR ID as a "list", (tabular file) using the NCBI SRA Tools - Extract reads in FASTQ/A format. Input type: List of SRA accession, one per line 2. Onc ...
written 9 months ago by scholtz60
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Comment: C: Data import from EBI SRA to Galaxy does not work
... Dear All, Some details to the workaround option suggested above (also, it seems to be faster than uploading from EBI): 1. Upload the SRR ID as a "list", (tabular file) using the NCBI SRA Tools - Extract reads in FASTQ/A format. Input type: List of SRA accession, one per line 2. Once uploaded, c ...
written 10 months ago by scholtz60
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Answer: A: Problems transferring FASTQ file from EBI to galaxy
... Hello, This is the reponse I received from the EBI folks to my inquiry - the problem will hopefully be resolved by next week :)) Cheers, Beata "On 2017.01.06., at 13:50, Marc Rossello mrosello@ebi.ac.uk wrote: Dear colleagues, The problems with the FTP servers that were limiting data downloads ...
written 11 months ago by scholtz60
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Answer: A: Data import from EBI SRA to Galaxy does not work
... Hello Mo, Thank you very much, I will try that for now. Also, this is the reponse I received from the EBI folks to my inquiry - the problem will hopefully be resolved by next week :)): "On 2017.01.06., at 13:50, Marc Rossello wrote: Dear colleagues, The problems with the FTP servers that were ...
written 11 months ago by scholtz60
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Data import from EBI SRA to Galaxy does not work
... Dear Galaxy Team, There seems to be a persistent problem with importing fastq files from EBI SRA - I've been trying to upload data since about Christmas, and keep getting the same error message as reported by others. Although the alternative "Extract reads in FASTQ/A format from NCBI SRA" works, t ...
galaxy data import ebi sra written 11 months ago by scholtz60 • updated 10 months ago by Jennifer Hillman Jackson23k
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Comment: C: Join genomic interval
... Hello Jen, Thank you very much! Beata ...
written 2.2 years ago by scholtz60
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Comment: C: Join genomic interval2
... Dear Bjoern, Thanks for getting back on this - I am a new user of Galaxy, and missed something trivial with the workflow: I had to convert the necessary files from tabular to interval, as it is actually suggested at the bottom of the page... Duh!! But I did not realize it until started to think how ...
written 2.2 years ago by scholtz60

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