Trinity Error, not recognizing read name formatting: [1]
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3.6 years ago

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 ---------------------

# 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