Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Run AVA/AVA-CLI without needing to specify MIDs

    Hi all

    Is it possible to run AVA (specifically command line AVA) without needing to specify an MID when creating the project. We have sff files that correspond to a single sample and have no barcoding information in them yet still want to use AVA to map these reads to a reference sequence and identify variants.

    Thanks for any suggestions

  • #2
    Yes its possible, you can ignore the MID section. But you'll need to specify your primers (forward and reverse) as well as what your reference sequences are.

    Comment


    • #3
      Originally posted by vamosia View Post
      Yes its possible, you can ignore the MID section. But you'll need to specify your primers (forward and reverse) as well as what your reference sequences are.
      Hi Vamosia
      I tried ignoring the MID section and specified the primers and reference also. But still not working. Are you saying about sequencing data in sff containing no any MID sequence? We have a sff file containing all MIDs sequences and then the sequence reads are extracted with individual MID. Each MID extracted sff file is then tried to align with reference sequence providing all primer information (forward reverse with start stop position) but we still get error " No Sample/Reference to align". What's wrong? Any suggestion please.....

      Comment


      • #4
        If your original sff file has MIDs, why are you splitting them ahead of time? You should leave them alone and demultiplex in AVA. Besides, when you split using sffinfo, you get fasta files not sff files, so assuming you are splitting with sffinfo then you're either wrong in your description of what you're doing (i.e. you're trying to use fasta files with AVA), or you're incomplete (i.e. after splitting the sff file, you used the resulting information in the fasta files to generate a matching set of sff files). Anyway sff files include data for every flow, including key and MID, regardless of whether they have been subsetted from a precursor file. The only difference is where the 5' trim point is set. But AVA doesn't respect the 5' trim point in sff files. So if you are using AVA, by definition you have to use sff files, and therefore you also have to deal with the MID regardless of if it's split or not. So why split.

        Comment


        • #5
          Originally posted by maven View Post
          If your original sff file has MIDs, why are you splitting them ahead of time? You should leave them alone and demultiplex in AVA. Besides, when you split using sffinfo, you get fasta files not sff files, so assuming you are splitting with sffinfo then you're either wrong in your description of what you're doing (i.e. you're trying to use fasta files with AVA), or you're incomplete (i.e. after splitting the sff file, you used the resulting information in the fasta files to generate a matching set of sff files). Anyway sff files include data for every flow, including key and MID, regardless of whether they have been subsetted from a precursor file. The only difference is where the 5' trim point is set. But AVA doesn't respect the 5' trim point in sff files. So if you are using AVA, by definition you have to use sff files, and therefore you also have to deal with the MID regardless of if it's split or not. So why split.
          Hi Maven ...
          Firstly, the precursor sff file is split using sfffile tool, i think, so the files i got are sff file, not fasta file, after splitting using individual MID. Also the the trim point is set to the base after the MID sequence after splitting. So I am still submitting sff file to AVA after extracting reading with MID. It still fails giving same error....But if I provide the MID, no error. The only difference is slightly different number of reads aligned to reference...I mean to say, if i run AVA precursor sff file..for MID1 the number of reads aligned is lets say 1000 then the number of reads aligned for MID1 sff file after splitting will be a bit less than 1000. However this is the point with MID information supplied to AVA. But I want to run AVA for sff files after splitting...without MID given. Each MID is correlated to a single sample, so want to run for single sample at a time....I am curious how vamosia ( his post up in this thread ) run skipping the MID section.....Thanks Maven...Waiting for Vamosia if he puts some light on this....

          Comment


          • #6
            Himalaya, you are right - totally on me for providing misinformation. However as you've discovered, you will still have to configure the MID in AVA and use a multiplexer because the MID is still in the read. BTW the OP said the sample had "no barcoding information", which may be why Vamosia said you can ignore the MID configuration. Anyway, good luck and sorry for steering you wrong with my misstatement about sfffile vs sffinfo.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM
            • seqadmin
              The Impact of AI in Genomic Medicine
              by seqadmin



              Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
              02-26-2024, 02:07 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 03-14-2024, 06:13 AM
            0 responses
            33 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-08-2024, 08:03 AM
            0 responses
            72 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-07-2024, 08:13 AM
            0 responses
            81 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-06-2024, 09:51 AM
            0 responses
            68 views
            0 likes
            Last Post seqadmin  
            Working...
            X