User: sierraallinone

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Posts by sierraallinone

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Comment: C: Differential expression analysis suggestions needed
... Hmm interesting.. a hybrid approach. I noticed they mentioned the alignment independent method works really well for unique transcripts. Just how unique? Because my transcripts are most likely going to be pretty similar with a few different alternative splicing zones of course it’s hard to tell sinc ...
written 21 days ago by sierraallinone10
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Differential expression analysis suggestions needed
... We have a trinity transcriptome assembly for 6 muscles types, 3 of which have triplicate data. We generated a supertranscript but now I’m reading conflicting things on how to approach the differential analysis portion of this experiment. We have no reference genome so if we go with HISAT2 —> cu ...
rna-seq written 21 days ago by sierraallinone10
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Comment: C: Detonate - Trinity De Novo Assembly Evaluator Error - invalid number of argument
... Here is the example they give: EXAMPLES We want to compute the RSEM-EVAL score for a contig assembly, 'assembly1.fa'. Our data are 76bp single-end reads contained in '/data/reads.fq'. The related species is human and 'human_transcripts.fa' contains all human transcripts. We use 8 t ...
written 23 days ago by sierraallinone10 • updated 23 days ago by Ram17k
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Comment: C: Detonate - Trinity De Novo Assembly Evaluator Error - invalid number of argument
... SYNOPSIS rsem-eval-calculate-score [options] upstream_read_file(s) assembly_fasta_file sample_name L rsem-eval-calculate-score [options] --paired-end upstream_read_file(s) downstream_read_file(s) assembly_fasta_file sample_name L rsem-eval-calculate-score [options] --sam/--bam [--pai ...
written 23 days ago by sierraallinone10 • updated 23 days ago by Ram17k
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Detonate - Trinity De Novo Assembly Evaluator Error - invalid number of arguments when trying to execute the rsem-eval-calculate score command
... I have paired-end Illumina Files named Mantle_TT_7_2_TGACCAqtrim.fq Mantle_TT_7_1_TGACCAqtrim.fq The 7_2 file being the forward and 7_1 being the reverse. The name of the Trinity Output Assembly file is `TrinityMantleTT.fasta` the paths to these files are: ~/Desktop/Mantle_TT_7_2_TG ...
rnaseq trinity detonate written 23 days ago by sierraallinone10 • updated 23 days ago by Ram17k
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Answer: A: Trinity Inchworm Error - what does it mean?
... So it turns out that this was a different error (Didn't scroll up far enough to see where it began--was using tmux) Here is the beginning of the error message: Number of Commands: 2 Use of uninitialized value $pm_temp in division (/) at /home/ubuntu/programs/Trinityrnaseq-v2$ 6.6/uti ...
written 23 days ago by sierraallinone10 • updated 23 days ago by genomax54k
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Comment: C: Trinity Inchworm Error - what does it mean?
... Here's the script: #!/bin/bash #This is a program to execute Trinity v2.6.6 using previously output trimmed files cd /home/ubuntu/programs/Trinityrnaseq-v2.6.6 perl Trinity --seqType fq --max_memory 976G \ --left /media/trinity_out/squid_trinity_out/Arm_WW_6_1_ACAGTG.fas ...
written 26 days ago by sierraallinone10 • updated 25 days ago by Ram17k
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Trinity Inchworm Error - what does it mean?
... I ran into this problem/error but I can't figure out the problem. We have 237G left of memory on our attached storage volume (where all the output goes). Is this a RAM limitation? If it indicates bad_alloc(), then Inchworm ran out of memory. You'll need to either reduce the size of your data set ...
rnaseq trinity inchworm error written 26 days ago by sierraallinone10
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Comment: C: Trinity Error encountered with thread, terminated abnormally, not all specified
... I was able to get it going again after I deleted some files off of the volume. The trimming was done within Trinity. ...
written 26 days ago by sierraallinone10
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Trinity Error encountered with thread, terminated abnormally, not all specified records have been retrieved.
... We had raw read files (20 million reads per file, paired end, 12 samples so 24 files in total) that we processed through trimmomatic within trinity and we are coming up with this error. From what I have read it seems to be a RAM issue. We have it set to 976G of RAM and 64CPU. We have tried looking a ...
trinity normalization rna-seq jellyfish written 29 days ago by sierraallinone10 • updated 12 days ago by Biostar ♦♦ 20

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Scholar 23 days ago, created an answer that has been accepted. For A: Trinity Inchworm Error - what does it mean?

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