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Comment: BRAKER3 genome annotation
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Buffo
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I suggest searching for the difference between structural annotation (identifying the coordinates of the ORFs in a sequence) and functional…
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looks good but I cannot find either Nupl2 nor Nup42 in the list!
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This table from Jackson labs that correlates many mouse identifiers with external databases will help. Look at the headers of the columns t…
Comment: Rename multiple fastq.gz files
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bk11
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I just gave hint in the comment above. Please try this, it should work for you.
#!/bin/bash
for file in `ls *fastq.gz`; do
f…
Comment: BRAKER3 genome annotation
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andorjkiss
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I also have this exact same question. I have my entire genome annotated and a braker.GTF file, but without protein "product" names.
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`Error: spawn vg ENOENT` means that Node could not find the `vg` command when it tried to run it. It got back [the `ENOENT` error code](htt…
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From 4.1.1 version, The utilities 'queryTaxonomyDatabase.pl' and 'queryRepeatDatabase.pl' are no
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Yeah, I heard that for cycle are not super suggested in R. I can't use tibble since my bone df has a different size than lung df..
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Can you show us the output from VEP and snpEff? They could be annotating two different transcripts.
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Honestly, any popular aligner will do: STAR, bowtie2, bwa, etc. Just make a FASTA file containing your sequences of interest, build an inde…
Comment: Rename multiple fastq.gz files
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Thank you! Just a stupid question, when I run this command it gives me the list of the names expected but does not actually change the name…
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BioinfGuru
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That's normal. Anything lower than the lower limit of R's numerical value range is rounded to 0. No resolution is required. Just be careful…
Answer: Rename multiple fastq.gz files
by
bk11
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This will be a very rough way of doing it-
#listing the fastq files
ls *fastq.gz
JM1-44589688_S693_L001_R1_001.fastq.gz JM110-…
Comment: RNAseq of primary tumor and metastases in two different organ
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on top of this I have many genes with a padj equal to zero, is this coming from an error or it's just that the value is too small for RStud…
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Honestly, use bwa mem like everyone else and call it a day.
bwa mem ref.fa X1.fq.gz X_2.fq.gz | samtools sort -o sorted.bam
See the b…
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