User: Jon17

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Jon1710
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Posts by Jon17

<prev • 15 results • page 1 of 2 • next >
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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 7 weeks ago by Jon1710
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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 9 weeks 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 9 weeks ago by Jon1710 • updated 9 weeks ago by h.mon25k
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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 21 months ago by Jon1710
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Comment: C: De-multiplexing Single Index BCL & Fastq reads?
... Thanks igor, so it should look like this? 61,,,,,CGATGTAT,,,, ...
written 21 months ago by Jon1710
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Comment: C: De-multiplexing Single Index BCL & Fastq reads?
... 2D = dual index? Assumptions are the mother of all screwups.... ...
written 21 months ago by Jon1710
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De-multiplexing Single Index BCL & Fastq reads?
... I have a mix of single index and dual index Illumina NextSeq reads mixed with dual index. The program bcl2fastq demultiplexed all of the dual index reads great, but I can't seem to figure out how to demultiplex single index reads. Suggestions / help wanted please! I'm interested in learning how t ...
illumina single-index bcl2fastq demultiplex written 21 months ago by Jon1710 • updated 21 months ago by h.mon25k
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Comment: A: Demultiplex fastq miseq reads
... Same problem but on a NextSeq with 6bp barcodes. All of these reads got dumped into "Undetermined_S0_L00X_RX_001.fastq.gz" How do I fix this? ...
written 21 months ago by Jon1710
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Comment: C: Best Tools for analyzing Bisulfite sequencing bam files?
... Is it throwing an error? **bioinformatics-cafe/bam2methylation.py --input sample1.proper.bam --ref /data1/nimblegen-pipeline/nimblegensoftware/config/epi-reference/hg19_chrY_PARs_masked.fa** > Methylation file: /tmp/tmp_bam2methylation_vUMnk8/read-F128.mpileup.txt samtools > view -u -F128 s ...
written 2.7 years ago by Jon1710
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Comment: C: Best Tools for analyzing Bisulfite sequencing bam files?
... Thankyou, i'm downloading it now. ...
written 2.7 years ago by Jon1710

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Popular Question 20 months ago, created a question with more than 1,000 views. For De-multiplexing Single Index BCL & Fastq reads?

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