User: eurioste

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eurioste40
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Posts by eurioste

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Visualizing BigWig is UCSC genome browser: link not available
... Ok, I found out what was missing, I had to edit the dataset attributes and manually add the Database/Build human hg19. This automatically made the UCSC link to appear. Thanks for the answers anyway. ...
written 8 months ago by eurioste40
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Comment: C: Visualizing BigWig is UCSC genome browser: link not available
... I'm using galaxy main, aligned the reads with BWA to hg19. ...
written 8 months ago by eurioste40
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Comment: C: Visualizing BigWig is UCSC genome browser: link not available
... Galaxy main, sorry for not being specific. Thanks. ...
written 8 months ago by eurioste40
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Visualizing BigWig is UCSC genome browser: link not available
... I wish to visualize some bigwig files generated from bamCoverage tools in the UCSC genome browser (human hg19) but unfortunately I see only the links for "display on IGV/IGB". I did this before but this time the link for the UCSC is missing. Do you know any work around? **EDIT:** Sorry for not bein ...
bigwig bam coverage visualization ucsc written 8 months ago by eurioste40
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Comment: C: BWA error [bwa_aln] 17bp reads: max_diff = 2
... Hello, I'm having a similar problem again, even while using the work around suggested, which was working until now: Fatal error: Exit code 134 () [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp reads: max_diff = 3 [bwa_aln] 64bp reads: max_diff = 4 [bwa_aln] 93bp reads: ma ...
written 8 months ago by eurioste40
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Filter SAM or BAM: "unknown reference name" when trying to select multiple chromossomes
... Hello, I aligned my reads to reference genome hg19 using BWA. I had to align to the full genome version because of errors with the hg19 canonical version. Now I want to filter out from my BAM all the reads aligned to non canonical chromosomes, unplaced contigs, and mitochondrial chromosome. I wish ...
bam samtools software error aligment written 9 months ago by eurioste40 • updated 9 months ago by Jennifer Hillman Jackson25k
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Comment: C: How to know if mapping to reference genome was succesful?
... Thanks for the answer but unfortunately these tutorials don't teach what I need. I've got got FastQC and pre-processing well covered and the tutorials only deal with deduplication and cross-sample correlations in post processing. I would like to have something like the distribution of MAPQ values or ...
written 9 months ago by eurioste40
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How to know if mapping to reference genome was succesful?
... Given a set of BAM files for single-end reads just mapped with BWA tool, how can I have an overview if the mapping will result in useful information and the quality of the mapping was good? These data is to be used in a ChIP-seq experiment. Because this is a pilot experiment there are no technical d ...
chip-seq bam mapping written 9 months ago by eurioste40
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BWA error [bwa_aln] 17bp reads: max_diff = 2
... I wish to align single end fastq sample using "Map with BWA" tool. The reads were trimmed several times with "Trim Galore" to remove specific adaptor sequences. The reads are 20-50 bp long. I'm using default parameters, except for the read group setting. But the run quickly fails at start giving th ...
software error bwa alignment written 9 months ago by eurioste40 • updated 9 months ago by Jennifer Hillman Jackson25k
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"An error occurred setting the metadata for this dataset"
... Hello, I'm just reporting I'm getting "An error occurred setting the metadata for this dataset" for almost all jobs, including simple jobs that previously worked with the data in my workflow, like FastQ groomer jobs. Because of this many jobs are getting stalled or having errors. ...
metadata software error written 15 months ago by eurioste40 • updated 15 months ago by Jennifer Hillman Jackson25k

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