paired ends show not the same count of reads cannot be assemble

[Jincheng Zheng]

Hi everyone,

     I encounter a problem about paired ends show not the same count of reads. When I download SRA formation data, and then use “fast-dump -I --spilt-files ” to generate left and right files. But I found the left and right files are not the same size. Also I used “fast-dump --split-files” ,“fast-dump --split-3” and "--defline-seq '@$sn[_$rn]/$ri' --split-files "got the same results. Then I used Trinity assemble them, and I failed. But in another paired ends data which left and right files have the same sizes, I success assemble them. So I want to know does it is the different sizes make me failed in assembling? Or something i missed? So I hope you can tell me what to do. Thank you!  

     Also, i have the second problem. When i assemble single end data using trinity. I never success. But i just use the code like assembling PE data and also i always success assembling PE data with same size in left and right. 

I use the code like:

./Trinity --seqType fq --max_memory 110G --single /home/p700/ncbi/public/transtdata/17/IlluQC_Filtered_files/SRRxxxxx    --CPU 12  

always got this:

----------- Jellyfish  --------------------

-- (building a k-mer catalog from reads) --

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

-- Skipping CMD: /home/p700/ncbi/public/transtdata/3/trinityrnaseq-2.2.0/trinity-plugins/jellyfish/bin/jellyfish count -t 14 -m 25 -s 16873085805  --canonical  single.fa, checkpoint exists.

-- Skipping CMD: /home/p700/ncbi/public/transtdata/3/trinityrnaseq-2.2.0/trinity-plugins/jellyfish/bin/jellyfish dump -L 1 mer_counts.jf > jellyfish.kmers.fa, checkpoint exists.

-- Skipping CMD: /home/p700/ncbi/public/transtdata/3/trinityrnaseq-2.2.0/trinity-plugins/jellyfish/bin/jellyfish histo -t 14 -o jellyfish.kmers.fa.histo mer_counts.jf, checkpoint exists.

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

--------------- Inchworm ---------------------

-- (Linear contig construction from k-mers) --

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

-- Skipping CMD: /home/p700/ncbi/public/transtdata/3/trinityrnaseq-2.2.0/Inchworm/bin//inchworm --kmers jellyfish.kmers.fa --run_inchworm -K 25 -L 25 --monitor 1   --DS  --num_threads 6  --PARALLEL_IWORM  > /home/p700/ncbi/public/transtdata/3/trinityrnaseq-2.2.0/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp, checkpoint exists.

-- Skipping CMD: mv /home/p700/ncbi/public/transtdata/3/trinityrnaseq-2.2.0/trinity_out_dir/inchworm.K25.L25.DS.fa.tmp /home/p700/ncbi/public/transtdata/3/trinityrnaseq-2.2.0/trinity_out_dir/inchworm.K25.L25.DS.fa, checkpoint exists.

Thursday, April 7, 2016: 19:42:32 CMD: touch /home/p700/ncbi/public/transtdata/3/trinityrnaseq-2.2.0/trinity_out_dir/inchworm.K25.L25.DS.fa.finished

ERROR, no butterfly assemblies reported. at ./Trinity line 1262.

[Jincheng Zheng]

When assemble single read data, the readcount always show :Error, cannot convert fastq file to fasta since cannot recognize read orientation as /1 or /2 (instead: A). Some time it is (instead: F). 

在 2016年4月7日星期四 UTC+8下午9:26:40，Jincheng Zheng写道：

[Brian Haas]

It might have something to do with the SRA conversion.  We have this to help:

https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-FAQ#ques_sra_fq_conversion

best,

~b

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--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas