User: luca.marisaldi

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Posts by luca.marisaldi

<prev • 15 results • page 1 of 2 • next >
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PITA troubleshooting for miRNA target prediction
... Hy guys, I am trying to run PITA (https://www.nature.com/articles/ng2135) on my own local computer (Ubuntu) for miRNA target prediction. I've got miRNAs and UTR sequences in .fa format. The program works well with examples provided and with other sequences. However, with such UTR sequences I've got ...
mirna pita target prediction written 11 weeks ago by luca.marisaldi30
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Trinity is not working..again?
... Hi all! Apparently there are troubles with trinity, again. The output of Trinity is an empty file so it doesn't produce an error. I paste here the first rows of the log in which there must be the error. > > Trinity version: v2.2.0 > -ERROR: couldn't run the network check to confirm lates ...
rna-seq trinity assembly written 16 months ago by luca.marisaldi30 • updated 16 months ago by Jennifer Hillman Jackson25k
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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 17 months 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 17 months 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 17 months ago by luca.marisaldi30 • updated 13 months ago by josefinagutierrezd10
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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 17 months 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 17 months 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 17 months 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 17 months 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 17 months ago by luca.marisaldi30

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