Questions tagged [illumina]

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Cromwell - controlling core/mem usage, and CallCaching, while running locally?

I'm sitting on a mountain of microarray (.idat files) data, and have been tasked to analyze it. I chose the MoChA pipeline, developed by the Broad Institute. It runs through Cromwell, of which I know ...
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Creating msk file for Illumina Array Analysis CLI Copy number train

recently I'm researching on how to detect CNV from Illumina microarray data. I found that Illumina has Array Analysis CLI software for this task, and I need to train the CN model myself, since the ...
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1 vote
0 answers
18 views

open source tools for CNV analysis from illumina SNP array

What are the best open source tools to analyse copy number variation using Illumina SNP array data...preferably R based tools, but open to other languages as well. I'm working with leukemia sample and ...
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3 votes
0 answers
24 views

Is there a generally accepted method used to impute missing DNA methylation data (probe beta-values)?

I'm looking at DNA methylation (DNAm) data such as TCGA (e.g., BRCA, KIRP, KIRC, etc.). Currently trying to build use my model to predict DNAm age on test sets, but many of the data sets are missing ...
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2 votes
1 answer
95 views

How to run MD5 check for multiple fastq files in different subdirectories?

I have received Illumina sequencing reads for 100 samples. I have 8 R1.fastq.gz and 8 R2.fastq.gz files for each sample in each ...
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34 views

Combine different FASTQ belonging to different hypervariable 16s regions

I'm really newbie in 16s microbiome analyses, so sorry for this question. I would like to perform a meta-analysis using only Illumina Amplicons sequences from different studies that have different ...
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1 answer
60 views

Understand this Kmer plot from Merqury?

The attached figure is generated based on Illumina reads from multiple individuals compared to genome assembly. Looks like there are a lot of kmers are reads only (grey colored). Also, a blue peak (2x ...
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1 vote
3 answers
81 views

Polishing PacBio or ONT with Illumina

Which tool would be good to polish PacBio or ONT with Illumina? Thank you in advance
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0 votes
1 answer
127 views

How to de novo hybrid assemble with Pacbio CCS and Illumina PE reads

I would like to perform de novo genome assembly on a diploid microalgal strain. I have two datasets: PacBio CCS/HiFi reads, low coverage. Illumina PE 2x150 (standard shotgun) Does anybody have any ...
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0 votes
0 answers
59 views

Why is bcl2fastq2 taking so long to calculate stats?

Our lab has been using bcl2fastq v2.20.0.422 to demultiplex RNA-seq data sequenced on an Illumina Novaseq machine on a beefy EC2 instance and we've run into the strange problem: namely that while ...
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  • 101
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0 answers
39 views

How to perform a meta-analysis using data consisting of paired-end and single-end reads generated from Illumina and Ion Torrent?

So basically I have RNA-seq reads that were generated from Illumina and Ion Torrent platforms for yeast species. I have seen an article where they compared liver cells of a rat that were sequenced ...
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1 vote
1 answer
371 views

What are some ways to error correct Oxford Nanopore long read sequencing?

I am sequencing long read genomic sequences to assemble MHC region haplotypes in a non model organism using Cas9 Sequencing Kit (SQK-CS9109) using flongle adaptors in the minION from Oxford Nanopore ...
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1 answer
41 views

Which format is the most raw format

I wanted information regarding which format is considered the most raw from an illumina sequencer ? fasta fastq bcl bam As per my research it should be bcl but I am not sure.
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0 votes
1 answer
48 views

polidy VCF file for Canvas somatic-wgs cnv calling

I am trying to run Illumina CANVAS cnv caller for Somatic-WGS. There is an option "--ploidy-vcf" which is mandatory to supply, but don't know what exactly that mean. I had supplied the CNV....
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1 answer
32 views

Modeling number of reads mapped to a gene

I am looking for a probability distribution of a number of reads mapped to a particular gene in metagenomic sequencing (NGS, shotgun, likely illumina). Naively one could model it via a binomial (or ...
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1 vote
1 answer
396 views

Error processing run file with bcl2fastq - Unable to open '.../RunInfo.xml' file for reading

I'm attempting to demux a nextseq run which I've successfully done several times in the past on other runs. I uploaded the run from my PC to the server (Ubuntu 18.04.4 LTS) without issue. Then I ran: <...
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2 votes
1 answer
61 views

Assembly reads having a copy of their beginning in their tail

I am analyzing the reads for the SARS-CoV-2 assembly with id SRR11140748. Apparently these reads were obtained with parallel sequencing by Illumina and Oxford Nanopore Technologies. I have found these ...
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2 votes
1 answer
44 views

Total read count of shotgun affected by few highly abundant sequences

I am building statistical models to analyse output from Illumina shotgun sequencing (HiSeq 4000) on stool samples (but RNA-seq data should behave similarily). The raw counts are a statistical sample ...
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3 votes
2 answers
1k views

How to demultiplex a mix of single-indexed and dual-indexed samples

The problem If I have a sample sheet that contains both single-indexed and dual-indexed samples, I can split it up into two sample sheets and then run bcl2fastq on each one. However, when doing this, ...
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2 votes
0 answers
638 views

What could cause differing counts of R1 and R2 in Paired End Sequencing (RNASEQ)

I recently finished mapping an RNAseq run using STAR2.3.0 and noticed the read1 and read2 counts are different, according to samtools flagstat. The map% is ~80% but the R1 R2 counts are: R1=...
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  • 591
4 votes
2 answers
144 views

How to predict stop codons in Illumina reads?

I have Illumina MiSeq paired-end reads from 150bp amplicons mapped to my reference genome (> 1000X coverage). These reads have indels that may or may not induce frameshifts. If the indel induces a ...
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3 votes
2 answers
963 views

Is there a safe catch-all adapter sequence for trimming?

I would like to trim/mark adapters using trimmomatic or picard MarkIlluminaAdapters from a series of Illumina Paired-End read fastqs. The fastq files may have been done using different kits or ...
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  • 309
3 votes
3 answers
267 views

Tools for quality trimming at 5 prime?

I'm looking for a tool that is capable to do quality trimming at 5' end and it is configurable. For example, I can choose the quality trheshold, the read length, etc. Any recommendations? I'm ...
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4 votes
2 answers
2k views

"Sequence Duplication Levels" module still fails after pre-processing Illumina data

I want to ask about why the sequence duplication levels are high after I trimmed by using Trimmomatic? I am using the following Trimmomatic operations: ...
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4 votes
2 answers
357 views

How to align output of grep --color=always? (To QC fasta/fastq files)

Grepping out short sequences from a fasta or fastq file is a really useful way to look at sequencing data. Using the option --color=always makes this even more ...
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2 votes
1 answer
1k views

Why are there more barcodes than GEMs in 10X chromium data?

Question: Why are there more barcodes than GEMs in 10X chromium data? Introduction I have several 10X genomics chromium libraries made with the de novo assembly/genome protocol. The 10X chromium ...
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  • 3,071
10 votes
3 answers
7k views

What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?

What is the index fastq file that comes with some Illumina sequencing datasets? (The samplename_I*.fastq.gz file.) For example, I recently received some 10X ...
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  • 3,071
7 votes
2 answers
1k views

What is the correct way to map Hi-C data with bwa mem?

Library Prep I have a Hi-C library prepped using an enzyme that cuts at GATC, so it leaves GATCGATC as the junction sequences. ...
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  • 3,071
1 vote
1 answer
61 views

How many reads do I need for hybrid assembly

I have Illumina and PacBio reads and I would like to use dbg2olc for hybrid assembly. Part of dbg2olc is SelectLongestReads which select reads that sum to ...
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1 vote
1 answer
70 views

Genotyping with Illumina HumanOmni1-Quad before whole genome sequencing

I read a paper about (whole genome sequencing analysis of 100 Southeast Asian Malays. It says "Prior to library preparation, each sample was genotyped on the Illumina HumanOmni1-Quad as an initial ...
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3 votes
3 answers
373 views

Relationship between sequencing lane and ngs dataset

I am fairly new to NGS data analysis and I am struggling to understand the exact relationship between a sequencing lane and an NGS dataset. I should add I don't work in the lab, I only do ...
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  • 173
5 votes
1 answer
3k views

Why do NEBNext indexing primers have sequence between the p5 oligo and index?

In a previous post I asked Why do NEB adapters have non-complementary sequence? Since then, I realized that there is some other sequence in the p5 indexing primer, as well as in the p7 indexing ...
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  • 3,071
5 votes
1 answer
141 views

Viral Metagenomics

I am analyzing viral metagenomics data (Illumina Miseq) for the first time. I have used Ray (reference below) for de novo viral genome assembly before but I haven't done metagenomics analysis before. ...
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  • 709
0 votes
1 answer
287 views

Get gene names corresponding to CPG probes

I have downloaded KIRC Methylation data (450K) using TCGA toolbox. The beta values given are with reference to CPG probes. Is there any package or function in R through which I can get the gene names ...
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  • 345
1 vote
1 answer
83 views

How to QC overamplified shotgun library?

I made some NEB ultra II whole-genome shotgun libraries with around ~200ng of template going into the indexing PCR step. The PCR was run for 13 cycles and I ended up having high library concentrations ...
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  • 3,071
6 votes
1 answer
61 views

SNP located within a promoter region (pig)

I have a couple of SNP identifiers such as MARC0073381 or ALGA0066960. The corresponding platform is Illumina Porcine SNP60 BeadChip (WG-410). I want to know if these SNP are located within a ...
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6 votes
2 answers
52 views

Does the MAPQ=0 fraction of a BAM file depend on the insert sizes?

When doing Illumina 2x150bp sequencing of genomic DNA, and after aligning the reads to GRCh38, does the percentage of the non-N fraction of the human genome as MAPQ=0 depend on the insert sizes of the ...
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  • 2,234
3 votes
1 answer
124 views

Scaffolding a genome with hybrid data

I am assembling a ~500MB genome, and have ~150x long reads and ~200x 150bp PE short reads, with a ~400bp insert size. I've done a lot of work with minimap+miniasm, and have what I think is a good set ...
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1 vote
2 answers
112 views

What are Approximate Read Counts (Library Sizes) and Lengths (Insert Sizes) for Next-Generation DNA Sequencers?

I am performing a simulation study and am curious about the parameters of my simulated metagenome. What are the library and insert sizes of some of the most "used" sequencers. Mainly, I am ...
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-2 votes
1 answer
39 views

Downloading CopyNumber450k package from Bioconductor

I am trying to download CopyNumber450k package in the R processor on my laptop in order to see if I could do a step of protocol for my research proffessor. I was unable to successfully download the ...
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3 votes
1 answer
224 views

genes with highest RPKM/FPKM for a human RNA-seq experiment?

Which genes/transcripts show up as having the highest RPKM/FPKM on a human RNA-seq experiment? Is it usually the same genes/transcripts? EDIT: mRNAs (e.g. poly-A RNA-seq preps) and not including ...
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  • 2,234
6 votes
1 answer
154 views

checks for spike-in sequence controls

I would like to know what do people verify when designing/using spike-in controls, to be used in sequencing experiments (mainly Illumina). So far I came up with this list: Does it align only to a ...
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  • 2,234
4 votes
1 answer
66 views

Analyzing Illumina Counts

I'm pretty new to all of this--forgive me if this is a simple question. When I download illumina counts from GEO (like the supplementary file in GSE89225). Can I do comparisons directly on that file?...
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5 votes
2 answers
322 views

GRCh38 centromeres mappability

Is the mappability of the centromeres in the GRCh38 genome reference similar to each other? As far as I can remember when GRCh38 came out, the sequence of the centromeres was determined by a ...
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  • 2,234
4 votes
3 answers
358 views

what percentage of the human genome is MAPQ=0?

When doing Illumina 2x150bp sequencing of genomic DNA, and after aligning the reads to GRCh38, what percentage of the non-N fraction of the human genome is MAPQ=0? This is, what part corresponds to ...
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  • 2,234