Trinity Error, not recognizing read name formatting: [1]
0
0
Entering edit mode
3.6 years ago
Shahzad ▴ 30

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
RNA-Seq De Novo Transcriptome Trinity Assembly • 2.8k views
ADD COMMENT

Login before adding your answer.

Traffic: 2286 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6