User: luca.marisaldi

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Posts by luca.marisaldi

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Trinity still not running
... I've got the same problem! Jobs seem not to proceed further than the 'waiting step'. Hope this report might help, Luca ...
written 1 day ago by luca.marisaldi30
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Comment: C: Trinity unusual error
... Hi Jen, well I run the job twice more after posting the question **without changing anything** (simply using the icon "run this job again") The last attempt was successful and Trinity proceeded further completing the run properly in both samples. For this reason I lost the info regarding the erro ...
written 3 days ago by luca.marisaldi30
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Trinity unusual error
... Hi all! I got twice the same error by running Trinity on Galaxy, that is: > Thread 1 terminated abnormally: Error, counts of reads in FQ: > 40001112.25 (as per cat /pylon5/mc48nsp/xcgalaxy/main_staging//15659867/inputs/dataset_19697450.dat > | wc -l) doesn't match fastool's report of FA r ...
galaxy assembly trinity software error rna-seq written 4 days ago by luca.marisaldi30 • updated 3 days ago by Jennifer Hillman Jackson22k
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Answer: A: Problem using data in different tools in galaxy
... Hello! Even if Galaxy can auto-detect the format properly (.fastq is let's say quite generic because would mean only sequences with scores) there are differences in quality score systems which in turns they could affects the format of the files. **Accordingly, it is always good to know to which ...
written 7 days ago by luca.marisaldi30
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Answer: A: TRINITY taking forever
... Hi Jennifer, I write you to report that once again, apparently, Trinity seems not working. Even if I did exactly what you said and also performed separately a small trial, **the Trinity step always shows "waiting to run".** Hope this issue is going to fixed soon because after almost a week of trou ...
written 8 days ago by luca.marisaldi30
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Answer: A: clear overrepresented reads that arent adaptadors
... Hello! Overrepresented sequences, among other things, might be an indicator of: - Contamination - Depending on the pre-processing cleaning might be a something related to an incomplete full elimination of ribosomal RNA - Presence of adapters (in this case FastQC should detect that) **I sugges ...
written 8 days ago by luca.marisaldi30
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Answer: A: rna seq read cleaning
... Hello! Did you check the quality of the reads before and after Trimmomatic cleaning/filtering ? FastQC is an excellent option and as far as I know **you can have a first check towards this kind of (supposed?) contamination by checking the section "Overrepresented sequences"**. Eventually you can q ...
written 10 days ago by luca.marisaldi30
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Answer: C: Graduate student learning to do RNAseq analysis
... Hello! Usually if the size of the files you want to upload is large (around 2 GB each) I strongly recommend to you to upload them through FTP! FileZilla is a good way to achieve that, it's easy to use and rather reliable. Once fully uploaded your files will appear on the "Choose FTP file" optio ...
written 10 days ago by luca.marisaldi30
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Comment: C: Waiting job doesn't run
... Hi Jennifer! First of all thank you for your help! However it's a pity to report that even after this correction there must be something wrong occurring again. **The assembly job did not start after your reply and even if I kept it queued during the whole Easter weekend (from Friday until today) ...
written 10 days ago by luca.marisaldi30
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Waiting job doesn't run
... Hi all! I started a workflow a couple of days ago after some trials I've done last weeks which took nearly a night to complete. This time with the same dataset and steps the workflow works until trinity then it stops, I mean the status is 'waiting to run' but in the end it doesn't seem to proceed f ...
workflow trinity written 16 days ago by luca.marisaldi30 • updated 15 days ago by Jennifer Hillman Jackson22k

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