Intrahepatic Cholestasis of Pregnancy

Frequently Asked Questions of Intrahepatic Cholestasis of Pregnancy (ICP)

ICP and Treatment Including SAMe

RNA-seq 5-prime to 3-prime Bias

Source of 3-prime Bias in PolyA-enriched RNA-seq

Cited from Figure 8: The use of 3′ bias as a quality control assay for cDNA.

"Total (bulk) RNA derived from tissue is confirmed to have a high RIN score before isolation of nuclei. Partial degradation of the RNA might occur during the preparation of nuclei by Dounce homogenization (nuclei prep) or FACS of the individual nuclei. If the mRNA is degraded by hydrolysis, shearing or RNases, truncated mRNA species could be created, and those containing the polyA sequence at the 3′ end of the transcripts might produce cDNA. This would generate greater RNA-seq coverage of the 3′ end of transcripts (3′-bias) compared with the high-quality bulk RNA."

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Cited from NGS Quality Control in RNA Sequencing- Some Free Tools

To visualise 5-prime or 3-prime bias, use the tools of Picard or RSeQC.

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Cited from How to understand median 5 prime to 3 prime bias ratio from Picard?

It is up to the analysis software to deal with 5-prime or 3-prime bias.

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Cited from  Salmon Doc

"--seqBias" to learn sequence bias

Salmon uses a variable-length Markov Model (VLMM) to model the sequence specific biases at both the 5’ and 3’ end of sequenced fragments. This methodology generally follows that of Roberts et al. [2], though some details of the VLMM differ.

Bash Parameter Substitution

Cited from How to tell if a string is not defined in a bash shell script?

• ${var+blahblah}: if var is defined, 'blahblah' is substituted for the expression, else null is substituted
• ${var-blahblah}: if var is defined, it is itself substituted, else 'blahblah' is substituted
• ${var?blahblah}: if var is defined, it is substituted, else the function exists with 'blahblah' as an error message.

Donwload SRA Files and Conversion to FASTQ Files

Tutorial: How to download raw sequence data from GEO/SRA

News: Ncbi Releases Entrez Direct, The Entrez Utilities On The Unix Command Line

Entrez Direct: E-utilities on the UNIX Command Line

What's the best way to download data from the SRA? Is it really this slow?

Downloading read and analysis data

Btrim: Fast Adapter Triming Tool

Cited from Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies

"A typical trimming of 30M reads with two sets of adapter pairs can be done in about a minute with a small memory footprint."

Btrim Readme

Remove rRNA from Fastq Files

Screen for rRNA contamination in RNA-seq data

PRO-seq and GRO-seq Data Analyses

PRO-seq Protocol

GRO-seq Data Analysis: Global analysis of transcription in castration-resistant prostate cancer cells uncovers active enhancers and direct androgen receptor targets

PRO-seq Data Analysis: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast

GRO-seq Data Analysis Chapter

Omics Tools: GRO-seq Analysis Tools

Strand-specific RNA-seq

Illumina Strand-Specific Library

Nature Methods Paper: Comprehensive comparative analysis of strand-specific RNA sequencing methods

How to tell which library type to use (fr-firststrand or fr-secondstrand)?