User: isu2017

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isu20170
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Posts by isu2017

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Comment: C: How Should I Trim My FASTQ File Now That I Merged Paired-End Reads
... I think that's probably what I'm going to end up doing, because the kit recommends trimming before any downstream analysis (and does not mention how to handle a situation like this.) Although I normally wouldn't really consider merging paired-FQ as "downstream", but we are interested in seeing how ...
written 5 months ago by isu20170
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How Should I Trim My FASTQ File Now That I Merged Paired-End Reads
... I have paired-end read files (fq_1 and fq_2.) Our kit mentions to trim them as follows: Trim 15BP from the right side (or 3" end) of read 1 (fq_1) and trim 15BP from the left side (or 5" end) of read 2 (fq_2.) seqtk trimfq -e 15 fq_1 > fq_1_trimmed seqtk trimfq -b 15 fq_2 > fq_2_tri ...
fastq paired-end written 5 months ago by isu20170
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Removing Human Contigs From Metagenomic Shotgun Assembly (FASTA)
... Hi there, I used SPADE to assemble my metagenome shotgun dataset into contigs. I just realized, however, that there is human contamination in this assembly. Because of how long the assembly took, I'm trying to think of ways to remove those human contigs from the FASTA assembly. Any suggestions? ...
spade metagenomics metagenome written 6 months ago by isu20170 • updated 5 months ago by theglobetrotter7830
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Sample Mouse RNA-Seq Dataset
... Anybody know where I can download a relatively small RNA-seq dataset I can use? Writing a pipeline, and just want small manageable dummy data to work with. Cheers! ...
rna-seq written 8 months ago by isu20170 • updated 8 months ago by EagleEye6.6k
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Exon-Spliced Graph vs Gene Model
... Hi everyone, I was wondering if anybody could clarify for this for me. I know of many papers where they create exon-spliced graphs based upon the output of software (such as Augustus.) My understanding was an exon-spliced graph just showcases the main isoform of a gene, in addition to any alterna ...
exon sequencing written 13 months ago by isu20170 • updated 13 months ago by pltbiotech_tkarthi180
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RNA-Seq DEGenes Without GTF
... I am working a specific species where we have a reference genome, and I was able to align our RNA-seq data to it. However, I am looking to create a count table to funnel our dataset to edgeR for DE analysis. I don’t have a GTF to use with something like HTSeq. Anybody have an idea of how to proc ...
rna-seq written 18 months ago by isu20170 • updated 18 months ago by RamRS26k
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Answer: A: Augustus Gene Frequency and Gene Names (Using BRAKER Pipeline)
... Any ideas would be greatly appreciative! ...
written 19 months ago by isu20170
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Augustus Gene Frequency and Gene Names (Using BRAKER Pipeline)
... Hi everyone, I recently finished running the braker pipeline on a previously unannotated organism. The pipeline just finished, with the final GTF file from Augustus being produced. However, the total amount of genes in his the file are much larger than what we expected (close to 100,000 were predi ...
augustus gene prediction braker written 19 months ago by isu20170

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