User: Jon17

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Jon170
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Posts by Jon17

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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 7 weeks ago by Jon170
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Comment: C: De-multiplexing Single Index BCL & Fastq reads?
... Thanks igor, so it should look like this? 61,,,,,CGATGTAT,,,, ...
written 7 weeks ago by Jon170
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Comment: C: De-multiplexing Single Index BCL & Fastq reads?
... 2D = dual index? Assumptions are the mother of all screwups.... ...
written 7 weeks ago by Jon170
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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 7 weeks ago by Jon170 • updated 7 weeks ago by h.mon9.0k
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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 7 weeks ago by Jon170
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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 12 months ago by Jon170
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Comment: C: Best Tools for analyzing Bisulfite sequencing bam files?
... Thankyou, i'm downloading it now. ...
written 12 months ago by Jon170
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Comment: C: Have variant call file, need to do snp counts (methylation counts)
... Alright I'll stop doing that. Thanks for the heads up. ...
written 12 months ago by Jon170
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Have variant call file, need to do snp counts (methylation counts)
... I'm using BisSNP to produce vcf files. Anyone know of a good way to calculate the following metrics? Any good tools to parse the VCF files? **TOTAL_C_IN_CpG_CONTEXT** Total number of C’s and C’s converted to T’s in capture target regions (this is sequence capture), both strands. **TOTAL_C_METH ...
methyl-seq bisulfite-seq written 12 months ago by Jon170 • updated 12 months ago by Biostar ♦♦ 20
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Best Tools for analyzing Bisulfite sequencing bam files?
... Once you have aligned bam file for Bisulfite sequencing what are the top tools for analyzing the alignments? bismark_methylation_extractor is one, what else? ...
bs-seq written 12 months ago by Jon170 • updated 12 months ago by WouterDeCoster22k

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