User: cwbenson1993

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Posts by cwbenson1993

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Answer: A: How to change fastq reads header for running Trinity on them?
... I have single end reads, so just needed to add a '/1' to my IDs that were generated by the samtools bam2fq command. sed gets confused adding the '/' (forward slash) character to a file. I did it with: awk '/^@HISEQ/ {$0=$0"/1"} 1' original.fq > newfile.fq This command looks for likes beg ...
written 3 months ago by cwbenson19930
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Comment: C: Sorting reads from host-pathogen interaction
... Fantastic! Thanks for all the help! ...
written 3 months ago by cwbenson19930
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Answer: A: Sorting reads from host-pathogen interaction
... Its the novel transcripts that im concerned about. If reads don't map to the fungus or the plant, then they correspond to a transcript that is specifically expressed at the host-pathogen interaction; either plant or fungus. For example, if I map infected grass reads to the fungal transcriptome and ...
written 3 months ago by cwbenson19930
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Comment: A: Sorting reads from host-pathogen interaction
... Hey lieven.sterck, Thanks for the response! Ive considered using BBsplit to further sort, but unfortunately I dont have genomic sequence of the plant. Does anyone know a tool that can sort RNA-seq data using the genome of one of the host-pathogen species? ...
written 3 months ago by cwbenson19930
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Sorting reads from host-pathogen interaction
... I am working on rna-seq data for a host-pathogen interaction between a grass species and its fungal parasite. The ultimate goal is to do differential expression analysis and functional enrichment to see what genes and pathways are involved in parasitism. I have: 1. Draft genome of the fungus 2. ...
assembly rna-seq written 3 months ago by cwbenson19930
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Comment: C: Trinity transcriptome quality assessment
... Hey Chris, thanks! I tried BUSCO for the longest gene isoform of both files but didn't get great number for either assembly... **With --jaccard_clip** C:74.4%[S:73.7%,D:0.7%],F:19.1%,M:6.5%,n:1335 **Without --jaccard_clip** C:73.3%[S:73.0%,D:0.3%],F:15.6%,M:11.1%,n:1335 ...
written 3 months ago by cwbenson19930
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Trinity transcriptome quality assessment
... I have 8 reps of illumina paired-end reads from a fungal RNA-seq experiment that I have *de novo* assembled using trinity. Trinity says to use the --jaccard_clip function if you predict high gene density, which may be the case for a small fungal genome. I assembled the transcriptome twice. Once ...
assembly rna-seq written 3 months ago by cwbenson19930 • updated 3 months ago by Chris Fields1.9k

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