User: will.schachterle

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United States
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5 years, 8 months ago
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6 years ago
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Posts by will.schachterle

<prev • 10 results • page 1 of 1 • next >
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Comment: A: Gene lists from RNA Seq and Chip Seq
... I'd like to split it up, so what are that chances that that those 24 upregulated genes happen to appear on the bound list, and 11 downregulated genes (there are 109 total downregulated genes) happen appear on bound list. ...
written 5.7 years ago by will.schachterle30
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Gene lists from RNA Seq and Chip Seq
... I have a list of genes that are up or downregulated after treatment, and another list of genes that are bound by a transcription factor. I want to know if the percentage of genes in the list of up/downregulated genes that also appears in the bound gene list is significant. I'm told that a Fisher's e ...
fisher's exact test chip-seq rna-seq written 5.7 years ago by will.schachterle30 • updated 5.7 years ago by komal.rathi3.6k
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Comment: C: highly variable FPKMs on small nucleolar RNAs and conf_lo=0 in cufflinks output?
... I'm relatively new to this, so I'm only on the main galaxy server and don't think I can add tools as a non-admin user. so, there's really no way to diagnose this without raw counts? I see that I can move over to another server (GVL-QLD looks good) that has an expanded numbers of tools, including HT- ...
written 5.9 years ago by will.schachterle30
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Comment: A: highly variable FPKMs on small nucleolar RNAs and conf_lo=0 in cufflinks output?
... I'm using galaxy so I'm sure how to just directly count reads. If I understand correctly, looking at the bam files in IGV should give me an idea about the raw counts. In the IGV grab I can see that there are similar number of reads across the different samples for Snord34, but again, for one sample ...
written 5.9 years ago by will.schachterle30
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highly variable FPKMs on small nucleolar RNAs and conf_lo=0 in cufflinks output??
... I'm using Galaxy to analyze some mouse RNA seq samples. I'm encountering a strange issue that I think is coming up in Cufflinks. This is a screenshot of my cufflinks settings. I'm getting weird FPKM values across different samples for a bunch of Snords and MIRs. For example, in one sample, these gen ...
galaxy cufflinks cufflink rna-seq written 5.9 years ago by will.schachterle30
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Answer: A: high discordant pair % with Tophat2 on Galaxy
... Mystery solved? I think the problem was the NGS: QC and manipulation->Filter FASTQ. It looks like Devon's suggestion that the samples were getting unpaired at the filtering step was correct. As I said, the quality of the reads looks fine to me, with #s >=33 from bp 1-51. So I guess I'll just s ...
written 6.0 years ago by will.schachterle30 • updated 5 months ago by RamRS27k
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Comment: C: high discordant pair % with Tophat2 on Galaxy
... I see PCT_CHIMERAS is, "The percentage of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes" so that sounds the same as discordant alignments. These are Qiagen prepped RNA samples from mouse ECs. The mapping is with mm9. I'm n ...
written 6.0 years ago by will.schachterle30 • updated 5 months ago by RamRS27k
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Comment: C: high discordant pair % with Tophat2 on Galaxy
... I did NGS: QC and manipulation > Filter FASTQ and set a min quality to 20. I see that there's a checkbox for "This is paired end data" and I'm pretty sure I checked that. But I can run this again, and be certain to check it. I don't actually think this filtering is really necessary because my rea ...
written 6.0 years ago by will.schachterle30
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Comment: A: high discordant pair % with Tophat2 on Galaxy
... The initial file format was fastqillumina - Input FASTQ quality scores type: Sanger + Illumina 1.8+ - Output FASTQ quality scores type: Sanger - Force Quality Score encoding: ASCII - Summarize input data: Summarize input ...
written 6.0 years ago by will.schachterle30 • updated 5 months ago by RamRS27k
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high discordant pair % with Tophat2 on Galaxy
... I'm totally new to all NGS tools so please bear with me. I've been trying to analyze data some paired reads with the tools on Galaxy. After "grooming" the FASTQ files, I attempted to map the reads with Tophat2, following the tutorial here (https://docs.uabgrid.uab.edu/wiki/UAB_Galaxy_RNA_Seq_Step_b ...
galaxy tophat2 rna-seq written 6.0 years ago by will.schachterle30

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