User: gupta

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gupta20
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1 year, 2 months ago
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g****@math.fu-berlin.de

Posts by gupta

<prev • 11 results • page 1 of 2 • next >
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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 5 weeks 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 5 weeks ago by gupta20
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Comment: C: Read length from HT-Seq
... Thank you so much Jen. Its really helpful :) ...
written 10 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 10 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 10 months ago by gupta20 • updated 10 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 11 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 11 months ago by gupta20 • updated 11 months ago by Jennifer Hillman Jackson22k
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Answer: A: RNor_6.0 assembly of rat genome - to add it to Galaxy
... Hello, For the option: Get data --> Upload file from your computer I still do not see 'RNor_6.0' in the options for Genome. Has this not yet been updated? Thanks. Best wishes, PG ...
written 11 months ago by gupta20
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Comment: C: Upload to the Galaxy ftp server
... No update on the problem yet..... ...
written 14 months ago by gupta20
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Comment: C: Upload to the Galaxy ftp server
... some more updates on the problem: - Finally, it took me two days and several tries to upload two files (3.4Gb each) to the ftp server. However, upload to the ftp server still fails when I try uploading new files. Until last Friday (11.03.2016), I had no problems in uploading files to the ftp serv ...
written 14 months ago by gupta20

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