User: gupta

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gupta20
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1 year, 4 months ago
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g****@math.fu-berlin.de

Posts by gupta

<prev • 14 results • page 1 of 2 • next >
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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 16 days ago by gupta20 • updated 16 days ago by Jennifer Hillman Jackson22k
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Comment: C: STAR --> option for reference genome
... Thank you so much Jen. I am using bosTau8. ...
written 6 weeks ago by gupta20
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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 7 weeks ago by gupta20 • updated 7 weeks ago by Jennifer Hillman Jackson22k
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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 3 months ago by gupta20
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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 3 months ago by gupta20
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Comment: C: Read length from HT-Seq
... Thank you so much Jen. Its really helpful :) ...
written 12 months ago by gupta20
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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 12 months ago by gupta20
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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 12 months ago by gupta20 • updated 12 months ago by Jennifer Hillman Jackson22k
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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 13 months ago by gupta20
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HTseq runs fail
... Hi, I am unable to execute HTseq on my data. I receive the following error message: 'This job was terminated because it used more memory than it was allocated.' I am currently using only 55% of the space allotted to my account on the Galaxy main server. Do I need more space to run HTseq? I would ...
galaxy rna-seq written 13 months ago by gupta20 • updated 13 months ago by Jennifer Hillman Jackson22k

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