Tag: bcl2fastq

empty fastq files created by docker bcl2fastq2 v2.20 OSX

empty fastq files created by docker bcl2fastq2 v2.20 OSX 0 HI, I installed a following docker image, REPOSITORY TAG IMAGE ID CREATED SIZE zymoresearch/bcl2fastq latest 037f216c2523 13 months ago 117MB and run a following command; docker run -d –name bcl2fastq -v /Volumes/Aura2/bcl_NU/170720_NB501488_0132_AH5V32BGX3:/mnt/run -v /Volumes/Aura2/output:/mnt/out zymoresearch/bcl2fastq:2.20 -R /mnt/run -o /mnt/out/Data/Intensities/BaseCalls/Alignment_1 –barcode-mismatches…

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Illumina summary.csv file units

Illumina summary.csv file units 1 We are using illumina Novaseq machines to do some sequencing and one of the files produced is a summary.csv file that has some info about the run that was sequenced. However, it is tough to figure out what units were used for a lot of…

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bcl2fastq with xGen Dual Index UMI Adapters to produce 3 read and 2 index fastqs

I usually remove Ns from the sample sheet and then run this command $ bcl2fastq -i Runfolder/Data/Intensities/BaseCalls -R Runfolder -o output_directory –sample-sheet Runfolder/SampleSheet.csv -r number_of_threads -p number_of_threads -w number_of_threads –no-lane-splitting –mask-short-adapter-reads 0 –use-bases-mask Y*,I8Y9,I8,Y* Original sample sheet: Sample_ID,Sample_Name,Description,index,I7_Index_ID,index2,I5_Index_ID,Sample_Project Sample1,Sample1,,TACCGAGGNNNNNNNNN,TACCGAGGNNNNNNNNN,AGTTCAGG,AGTTCAGG,BRCA1 Sample2,Sample1,,CGTTAGAANNNNNNNNN,CGTTAGAANNNNNNNNN,GACCTGAA,GACCTGAA,BRCA1 Formatted sample sheet: Sample_ID,Sample_Name,Description,index,I7_Index_ID,index2,I5_Index_ID,Sample_Project Sample1,Sample1,,TACCGAGG,TACCGAGG,AGTTCAGG,AGTTCAGG,BRCA1 Sample2,Sample1,,CGTTAGAA,CGTTAGAA,GACCTGAA,GACCTGAA,BRCA1 Our RunInfo.xml file looks…

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BCL files conversion to FASTQ without SampleSheet.csv

BCL files conversion to FASTQ without SampleSheet.csv 1 Dear community, I have got NGS data which is basically the BaseCalls folder with .bcl files. I want to know how to successfully convert .bcl files to .fastq format. So far, I have been using the bcl2fastq program, however, I have no…

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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 demultiplexing is very fast, generating the stats files are unbearably slow. In a recent example, we demultiplexed one…

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Troubleshooting Tips – bcl2fastq creates duplicate reads

Forum:Troubleshooting Tips – bcl2fastq creates duplicate reads 1 Hi, I have seen a few times where bcl2fastq (v2.20) will produce duplicate FASTQ entries in sequencing read IDs, raw sequences, & quality scores. This causes issues with downstreams tools like Picard MarkDuplicates (e.g. Exception in thread “main” htsjdk.samtools.SAMException: Value was put…

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Get failed reads on Novaseq

Get failed reads on Novaseq 0 Dear all, on a NextSeq550, I can get failed reads (not PF) with –with-failed-reads using bcl2fastq. With the more modern bclconvert software, this does not exist. support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html Also, it seems failed reads are not saved any more by the Novaseq, which is problematic for…

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How to fasterq-dump 10x genomics snATACseq fastq from SRA

How to fasterq-dump 10x genomics snATACseq fastq from SRA 2 I am trying to retrieve fastq files from a 10x genomics snATACseq dataset on SRA. Each run should have 4 fastq files associated with it: I1: Dual index i7 read (optional) R1: Read 1 R2: Dual index i5 read R3:…

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bcl2fastq ERROR

bcl2fastq ERROR 1 Hi all, I have a problem. I’m running bcl2fastq software on Ubuntu, but I can’t demultiplex anything as the software gives me this error: *ERROR: bcl2fastq::common::Exception: 2021-Sep-02 12:12:34: Success (0): /home/Software/bcl2fastq/src/cxx/lib/layout/Layout.cpp(693): Throw in function void bcl2fastq::layout::handleDefaultSample(bool, bool, size_t, bcl2fastq::layout::LaneInfo&, bool&) Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::InputDataError> std::exception::what: Missing a…

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