Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Testing bcl2fast

    Hello everybody!

    I'm new at the NextSeq world, my lab just bought a new machine some weeks ago and now I will be responsible to set up all the environment to perform different bioinformatics analysis

    The first i did was compile bcl2fastq in our cluster, I had no problem with it. Now i would like learn how does it works


    I found some bcl files at the piccard GitHub https://github.com/broadinstitute/picard

    but I'm not sure that I have all the archived required here, for example i do not have the SampleSheet file

    so my questions are:

    1- How do I can execute the bcl2fastq script. Do i have enough with

    bcl2fastq --input-dir xxxx --ouput-dir xxxx

    2 which files should i place to the input-dir? Do I have enougt with the bcl file or do i have to place some other files there? What if i don't have the SampleSheet file?

    p

  • #2
    Which sequencer are you getting? bcl2fastq v.2.16.x is required for NextSeq and Hiseq X data. If you are getting a MiSeq/HiSeq 1xxx/2xxx machine then you will want to use bcl2fastq v.1.8.4. The conversion programs included in these two versions are different and have different command syntax.

    Quote from Illumina.

    The bcl2fastq2 v2.16 software can be used to convert BCL files from all Illumina sequencing systems running RTA version 2.0 and above. This is a change from the original information, which indicated that v2.16 could be used with all sequencers running RTA 1.18 and above: that information is no longer correct. For conversion of data generated on Illumina sequencing systems using versions of RTA before RTA 2.0, use bcl2fastq v1.8.4.

    Comment


    • #3
      we have the Ilumina NextSeq 500 and our provider told me to use this software



      the point now is hos do i use it.

      thanks

      Comment


      • #4
        You are using the right software.

        You will need full data folder produced by the sequencer for a real test. I am not sure if you can download a full flowcell data folder to test the software. Check on BaseSpace.

        Possible fastq conversion command will look like this. Demultiplexed data is going to be put in "Unaligned" directory. Following command is using 4 cores. There is no big benefit to going overboard with # of cores.

        Code:
        $ bcl2fastq -i /path_to/flowcell_ID/Data/Intensities/BaseCalls -o /path_to/flowcell_ID/Unaligned -r 4 -d 4 -p 4 -w 4
        You can run

        Code:
        $ bcl2fastq -h
        to get help on all possible command line options.

        I believe you can specify a separate location for the samplesheet file with v.2.16. Previously SampleSheet.csv file had to be inside the /flowcell_ID/Data/Intensities/BaseCalls directory. That option would likely be specified with --samplesheet /path_to/samplesheet.csv addition to above command line (I have not tested the 2.16 version yet).

        You can create an example samplesheet by using Illumina Experiment Manager (v.1.9) program that you can download from Illumina support site. This is a windows program.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Advanced Methods for the Detection of Infectious Disease
          by seqadmin




          The recent pandemic caused worldwide health, economic, and social disruptions with its reverberations still felt today. A key takeaway from this event is the need for accurate and accessible tools for detecting and tracking infectious diseases. Timely identification is essential for early intervention, managing outbreaks, and preventing their spread. This article reviews several valuable tools employed in the detection and surveillance of infectious diseases.
          ...
          11-27-2023, 01:15 PM
        • seqadmin
          Strategies for Investigating the Microbiome
          by seqadmin




          Microbiome research has led to the discovery of important connections to human and environmental health. Sequencing has become a core investigational tool in microbiome research, a subject that we covered during a recent webinar. Our expert speakers shared a number of advancements including improved experimental workflows, research involving transmission dynamics, and invaluable analysis resources. This article recaps their informative presentations, offering insights...
          11-09-2023, 07:02 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 12-01-2023, 09:55 AM
        0 responses
        21 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 11-30-2023, 10:48 AM
        0 responses
        20 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 11-29-2023, 08:26 AM
        0 responses
        14 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 11-29-2023, 08:12 AM
        0 responses
        17 views
        0 likes
        Last Post seqadmin  
        Working...
        X