User: MAPK

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MAPK1.1k
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Posts by MAPK

<prev • 331 results • page 1 of 34 • next >
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Answer: A: Trinity assembly error
... Ok. I finally figured out the problem for this: Trinity works well with Java version 7. So before running Trinity, we need to make sure we set java version 7 like this: To get a list of your installed Java platforms, run the following command from the terminal: `sudo update-alternatives --config ...
written 13 days ago by MAPK1.1k
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Comment: C: Trinity assembly error
... Additionally, it is generating the same error for the test fastq files from the Trinity package itself. I tried `make test_trinity` and it is generating the same error. ...
written 13 days ago by MAPK1.1k
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Comment: C: Trinity assembly error
... Thanks. Yes, the two files are part of paired reads from `fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files *.sra` option generating left and right fastq files. ...
written 13 days ago by MAPK1.1k
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Trinity-v2.5.1 assembly generating bowtie 2 error
... Hi I am running Trinity (Trinity-v2.5.1) invoking the following command : Trinity --seqType fq --max_memory 100G --right /media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal-mycovirus/sra/SRR915897/SRR915897_1.fastq --left /media/owner/b54f3251-5380-4288-9ddf-fa3357ea8294/mycorrhizal-m ...
rnaseq trinity written 13 days ago by MAPK1.1k
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Trinity assembly error
... Hi All, I am running this assembly using Trinity feeding the following command: Trinity --seqType fq --max_memory 100G --right file_1.fastq --left file_2.fastq --CPU 16 --output SRR-trinity-output However, it keeps generating this error shown below. Can someone please help me resolve th ...
rnaseq written 14 days ago by MAPK1.1k
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Possible evolutionary studies using whole genome and RNA-seq data
... Hi All, I have created this post to explore all the possible studies one could carry out with whole genome and RNA seq data for an organism. Could you please list all the possible studies we can carry out if we have (from a single organism): 1. Whole genome data 2. RNA-seq data 3. Both ...
rnaseq written 14 days ago by MAPK1.1k
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Comment: C: SRA data sets and runs
... Is it ok if I merge all fastq files extracted from these 36 runs of SRA files and do a single analysis? ...
written 14 days ago by MAPK1.1k
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Comment: C: SRA data sets and runs
... Thanks to both of you ...
written 15 days ago by MAPK1.1k
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SRA data sets and runs
... Hi All, I am looking at this RNA-seq data [here][1]. I want to know which specific run do I need to select from as there are 36 different runs starting from SRR id SRR3285884 to SRR3285919. I want to assemble this specific transcriptome data using Trinity for my research and I am not sure which run ...
rnaseq sra written 15 days ago by MAPK1.1k
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Comment: C: Authorship conflict and resolution
... I did try to delete it after reading all of your comments, especially Emily's comment. I don't want anyone from my previous group to see this post now. Thanks to all who contributed in this discussion. ...
written 4 weeks ago by MAPK1.1k

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