User: gupta

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gupta30
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3 months, 1 week ago
Joined:
2 years, 5 months ago
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g****@math.fu-berlin.de

Posts by gupta

<prev • 15 results • page 1 of 2 • next >
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Unable to view HTML FASTQC files at https://usegalaxy.org -- Please follow for updates
... Hello, I am unable to view all my old 'FASTQC **html** files' on the galaxy main server. There is no problem in viewing the 'FASTQC text files'. Can the error be due to recent Galaxy upgrade? I would be grateful if the problem could be resolved. Thank you. Best wishes. Pooja ...
usegalaxy.org galaxy fastqc html display written 3 months ago by gupta30 • updated 3 months ago by Jennifer Hillman Jackson25k
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Cufflinks output empty
... Hi, I am encountering a problem similar to that mentioned here: https://www.biostars.org/p/45848/ I am on the main Galaxy server. I have 6 samples, and Cufflinks worked fine for 4 samples. The other two samples return an 'empty output'. I am running Cufflinks without any input annotation file and ...
galaxy main cufflinks written 13 months ago by gupta30 • updated 13 months ago by Jennifer Hillman Jackson25k
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Comment: C: STAR --> option for reference genome
... Thank you so much Jen. I am using bosTau8. ...
written 14 months ago by gupta30
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STAR --> option for reference genome
... Hi, I have been trying to test RNA-Star on the Galaxy main server, but in the option for 'Select reference genome', no species appears in the drop-down list. Is this bug only encountered by me or is it a general issue? I would be thankful for any help and comments. Best wishes, PG ...
galaxy star rna-seq written 14 months ago by gupta30 • updated 14 months ago by Jennifer Hillman Jackson25k
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Trim Galore version - Adapter sequence
... Hello, I have been using Galaxy's Trim galore for clipping adapters from Illumina small RNA sequences. While using automatic adapter detection, I noticed that the adapter being removed is 'ATGGAATTCTCG'. However, in Trim galore's change log from 2015 it is mentioned: *** 12-11-15: Version 0.4.1 re ...
trim galore small rna adapter rna-seq written 16 months ago by gupta30
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Comment: C: Jobs as grey history
... Even I am experiencing a similar problem. I started Cuffdiff, but the history item remains gray with an exclamation mark. I would be extremely thankful if the problem can be resolved. Thank you. PG UPDATE: My submitted jobs were processed. Now it worked for me. ...
written 16 months ago by gupta30
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Comment: C: Read length from HT-Seq
... Thank you so much Jen. Its really helpful :) ...
written 2.1 years ago by gupta30
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Answer: A: cuffdiff tabular file conversion
... Hi, You should be able to open the tabular file directly in excel. Make sure to enter the appropriate delimiter for your data (e.g. 'tab') while opening it in excel. ...
written 2.1 years ago by gupta30
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Read length from HT-Seq
... Hi, Sorry for asking this very basic question. I have paired-end RNA-Seq data. After initial adapter and quality trimming, I used Tophat for alignment. Later, I obtained the read count using HT-Seq from the alignment file. My questions is: Can I also somehow obtain the length of the reads that wer ...
rna-seq ht-seq written 2.1 years ago by gupta30 • updated 2.1 years ago by Jennifer Hillman Jackson25k
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Comment: C: HTseq runs fail
... I read previous posts regarding this error, and tested the suggestions on my problem, i.e. * Re-runs - I performed re-runs. * Input/parameter adjustments - There are not many parameters associated with this software that can be modified to reduce the memory requirement. RESULT --> It still fa ...
written 2.2 years ago by gupta30

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