Question: Trinity Error, not recognizing read name formatting: [1]
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gravatar for Shahzad
28 days ago by
Shahzad10
Pakistan
Shahzad10 wrote:

I am using Trintiy to make transcriptome assembly and it looks like something is wrong with my sequence format. I am using this data by downloading it from GEO database and SRA files are not available for this project. So, I cant use fastq-dump (if that is why it is behaving like this). Please let me know any possible solution for this error (mentioned in the title.

Thank you


-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------


------------ In silico Read Normalization ---------------------

-- (Removing Excess Reads Beyond 50 Coverage --

running normalization on reads: $VAR1 = [

      [
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794483_C1_R1_1.fq',
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794484_C1_R2_1.fq',
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794485_C1_R3_1.fq',
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794486_C2_R1_1.fq',
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794487_C2_R2_1.fq',
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794488_C2_R3_1.fq'
      ],
      [
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794483_C1_R1_2.fq',
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794484_C1_R2_2.fq',
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794485_C1_R3_2.fq',
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794486_C2_R1_2.fq',
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794487_C2_R2_2.fq',
        '/gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794488_C2_R3_2.fq'
      ]
    ];

Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -A /gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794483_C1_R1_1.fq >> left.fa CMD: seqtk-trinity seq -A /gpfs1/scratch/30days/uqmiqbal/myrnaexp/GSM794483_C1_R1_2.fq >> right.fa Error, not recognizing read name formatting: [1]

If your data come from SRA, be sure to dump the fastq file like so:

    SRA_TOOLKIT/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files file.sra

Error, not recognizing read name formatting: [1]

If your data come from SRA, be sure to dump the fastq file like so:

    SRA_TOOLKIT/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files file.sra
ADD COMMENTlink modified 27 days ago • written 28 days ago by Shahzad10
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