User: Jon17

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Jon1710
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Posts by Jon17

<prev • 21 results • page 1 of 3 • next >
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Detecting GC Bias in Transcriptomes (RNA-seq)
... What's the best way to detect GC bias in a transcriptome (RNA-seq)? We are currently aligning to a regular genome fasta file (like hg38) but that means there are skips in the coverage. exon -- intron -- exon..... I know how to calculate GC bias of individual exons. Bedtools and R is a huge ...
rna-seq transcriptome written 10 weeks ago by Jon1710
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Comment: C: rnaseqc.v2.3 - Doesn't detect exons in GTF
... I think I solved the situation. Still investigating but at least I'm getting output now. Will post an update later. ...
written 11 weeks ago by Jon1710
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Comment: C: rnaseqc.v2.3 - Doesn't detect exons in GTF
... I think so. I've ran the bam file against both the original gencode gtf file and a modified version where I converted the "chr2" to just "2". Basically just removing all of the "chr" from the 1st column. I still have issues. Legend for the text below: **Column 1 = Bam file** (samtools view | awk ...
written 11 weeks ago by Jon1710
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rnaseqc.v2.3 - Doesn't detect exons in GTF
... RNASeqc doesn't like any of my GTF files. I have no problem running the example dataset. Any idea why? When I run this: rnaseqc.v2.3.4.linux gencode.v29.compressed-noGene.gtf NuGen_mRNA_10_ERCC2_2_md.bam OUTPUT I get this result: There were either no genes or no exons in the GTF 0 ...
mit qc rna-seq gencode written 11 weeks ago by Jon1710 • updated 11 weeks ago by RamRS24k
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Comment: C: Graphing GC Bias in Sequence Capture
... Yeah I'm working on it. I had no idea if the software actually worked when I said thank you. I just finished processing a data-set and it worked. ...
written 4 months ago by Jon1710
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Comment: C: Graphing GC Bias in Sequence Capture
... Thank you!!!!!!!!!!!!!!!!! ...
written 4 months ago by Jon1710
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Graphing GC Bias in Sequence Capture
... Anyone have recommendations for making a chart like this for sequence capture? Picard CollectGcBiasMetrics only works for whole genome analysis. Picard hsMetrics tends do do funny things with window sizes. I've had some success with a bedtools & custom scripting but can't reproduce other peop ...
bed picard gcbias sequencing written 6 months ago by Jon1710 • updated 4 months ago by trausch1.4k
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Comment: C: Compute mean depth coverage for exome data with paired end, overlapping, feature
... What version of bedtools is that? Version: v2.17.0 doesn't have the "-mean:" option. only -hist nevermind, found it in v2.27.1 ...
written 6 months ago by Jon1710
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Depth of coverage of Bed file regions?
... Best way to find average depth of coverage for very specific regions via a bed file? I've tried this: bedtools genomecov -i $BED -ibam $BAM But my bam file says this: > chr1 69090 69190 > chr1 69190 69290 > chr1 69290 69390 > chr1 69390 69490 and the output is this: ...
bedtools bed coverage genome written 6 months ago by Jon1710 • updated 6 months ago by h.mon27k
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Picard HsMetrics on Whole Genome (no bedfile) need "HS_Penalty_20X & HS_LIBRARY_SIZE"
... Is there a way to get these metrics on a whole genome scale? I might do a hack where I create a bed & interval files covering the entire genome. - **HS_Penalty_20X** - "hybrid selection penalty" incurred to get ***80%*** of target bases to ***20X***. - **HS_LIBRARY_SIZE** - estimated number ...
gatk picard written 2.1 years ago by Jon1710

Latest awards to Jon17

Popular Question 6 months ago, created a question with more than 1,000 views. For Full Size Bismark Test Dataset? Industry standard methods for Sequence capture
Popular Question 2.1 years ago, created a question with more than 1,000 views. For De-multiplexing Single Index BCL & Fastq reads?

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