User: lucas.caue.jacintho

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Posts by lucas.caue.jacintho

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Fusion detection tool error (STAR-fusion, STAR-SEQR,arriba)
... Hi everybody, I am having some problems with fusion detection tools. Some of the most used ones, like STAR-Fusion STAR-SEQR required a CTAT-library, but I have a custom genome which I would like to use for my fusion detection, I follow the instructions found at CTAT repository https://github.com/NCI ...
ctat fusion detection star arriba rna-seq written 9 months ago by lucas.caue.jacintho30 • updated 8 months ago by Baoxu0
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Comment: C: Running STAR with --twopassMode Basic
... Hi caggtaagtat, thank you so much about your very elaborated reply! It seems that this really help with this error! ...
written 9 months ago by lucas.caue.jacintho30
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Comment: A: Running STAR with --twopassMode Basic
... Hi guys, Just a update: I tried both suggestions: I try to run the `SLURM` with the `--exclusive` tag, and I also try to run with a reduced number of cores. I still have the same Log.out error, and then and I tried to use `ulimit -v` and `ulimit -n` the STAR crash yet. If someone has any insight a ...
written 9 months ago by lucas.caue.jacintho30
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Comment: C: Running STAR with --twopassMode Basic
... Hi!Thanks for your reply. By "no successs" I meant that the limits were changed and STAR crashed anyway. I will try to lower the number of threads ...
written 9 months ago by lucas.caue.jacintho30
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Comment: C: Running STAR with --twopassMode Basic
... Exactly, my cluster uses `SLURM`, when I ran `top` and `htop` seem that I am the only one using that, i gonna try to open a new session with `--exclusive` and see what I get ...
written 9 months ago by lucas.caue.jacintho30
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Comment: C: Running STAR with --twopassMode Basic
... Hi, i am using the interactive mode into the cluster and not a bash script (I do not know if that is the answer to your question). For initiate the interactive mode I request the resources as this way: `srun --pty -p interactive --mem 250G -c 20 -t 0-12:00:00 /bin/bash` ...
written 9 months ago by lucas.caue.jacintho30
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Running STAR with --twopassMode Basic
... Hi everybody, I am running STAR without and with the command `--twopassMode Basic`. In the first option I could run with no problems, but then and I tried to use the `--twopassMode` and I got a fatal error as below: >EXITING: fatal error trying to allocate genome arrays, exception thrown: std::b ...
star rna-seq ulimit written 9 months ago by lucas.caue.jacintho30 • updated 9 months ago by caggtaagtat1.1k
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Comment: C: Visualizations of chimeric connections in different chromosomes
... Thanks for your useful suggestion!I am trying to use your tool, but actually I am having some trouble to run the algorithm, I am not sure but maybe because i am dong RNAseq and not NGS. If you have any clue what is happening I'd appreciate it! T ...
written 9 months ago by lucas.caue.jacintho30
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Visualizations of chimeric connections in different chromosomes
... Hi everybody, I just did a alignment by STAR, and I am pretty sure the BAM output has some chimeric connections among different chromosomes, but I do not know how to visualize them, whereas I do see the chimeric conections in the same chromosome. is this something related to the samples being pa ...
assembly igv inter-chromosomal chimeric junction written 9 months ago by lucas.caue.jacintho30 • updated 10 weeks ago by Jim Robinson280
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Comment: C: Hisat2 splice sites extract blank files
... That's fair. So what is the solution? use a txt file made by myself with `--known-splicesite-infile ` ? Because, I think I am not supposed to have novel splice junctions or new junctions annotations if I do not provide any file like those ones. ...
written 12 months ago by lucas.caue.jacintho30

Latest awards to lucas.caue.jacintho

Student 8 months ago, asked a question with at least 3 up-votes. For Fusion detection tool error (STAR-fusion, STAR-SEQR,arriba)

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