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Comment: Comment: Which companies/institutions allow you to use their servers for bioinformatics a
3.5 years ago by kristina.mahan ▴ 180
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2.5k
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Comment: Comment: Which companies/institutions allow you to use their servers for bioinformatics a
3.5 years ago by kristina.mahan ▴ 180
6
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6
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2.5k
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Which companies/institutions allow you to use their servers for bioinformatics analysis?
pacbio isoseq
updated 2.9 years ago by 45k • written 3.5 years ago by ▴ 180
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1
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1.4k
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How do I get a gtf file to use rnaQUAST
rnaQUAST ensembl gencode gtf gff
updated 3.8 years ago by ▴ 90 • written 5.0 years ago by ▴ 180
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4
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1.7k
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Do you need a genome or can a transcriptome alone be used to identify biosynthetic pathways? Why sequence and assemble a genome?
de-novo-assembly biosynthetic-pathways plant transcriptomics
updated 2.1 years ago by 45k • written 3.9 years ago by ▴ 180
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1
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1.7k
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Comment: Comment: Do you need a genome or can a transcriptome alone be used to identify biosynthet
3.9 years ago by kristina.mahan ▴ 180
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0
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593
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Can plantiSMASH be used with a transcriptome instead of a genome?
plantiSMASH
updated 2.1 years ago by 45k • written 3.9 years ago by ▴ 180
1
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3
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1.7k
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Genewiz gave me bam files instead of fasta files- can I convert bam to fasta to have a genome assembly?
bam samtools fasta
updated 2.1 years ago by 45k • written 4.2 years ago by ▴ 180
3
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2
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1.6k
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Will this de novo transcriptome assembly be useful in looking at RNAseq differential expression?
de-novo-assembly
updated 2.1 years ago by 45k • written 4.3 years ago by ▴ 180
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4
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2.6k
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How do you add gene annotations from a Diamond Blastx tsv file to a csv file with RNAseq differential expression data?
BLASTx RNA-seq diamond
updated 2.1 years ago by 45k • written 4.3 years ago by ▴ 180
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Comment: Comment: How do you add gene annotations from a Diamond Blastx tsv file to a csv file wit
4.3 years ago by kristina.mahan ▴ 180
0
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1
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2.3k
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Comment: Comment: What Coverage allele-fraction threshold to use?
4.6 years ago by kristina.mahan ▴ 180
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1
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2.3k
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Comment: Comment: What Coverage allele-fraction threshold to use?
4.6 years ago by kristina.mahan ▴ 180
0
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5
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2.3k
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What Coverage allele-fraction threshold to use?
allele-fraction snps
updated 2.1 years ago by 45k • written 4.6 years ago by ▴ 180
3
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2
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1.9k
views
How to check for completeness of a mitochondrial or chloroplast genome?
genome-completeness organelles
updated 2.1 years ago by 45k • written 4.7 years ago by ▴ 180
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1.9k
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Answer: A: How to check for completeness of a mitochondrial or chloroplast genome?
4.7 years ago by kristina.mahan ▴ 180
0
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1
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2.3k
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Convert .sqn file to .gbk
organelle
updated 2.1 years ago by 45k • written 4.7 years ago by ▴ 180
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0
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1.4k
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Comment: C: How to obtain organelle genome
4.7 years ago by kristina.mahan ▴ 180
5
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9
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5.8k
views
Error when trying to run IGV on server
igv
updated 4.3 years ago by ▴ 140 • written 6.2 years ago by ▴ 180
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0
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911
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Need to fix .sqn genome annotation file prior to uploading to NCBI
sqn NCBI
updated 2.1 years ago by 45k • written 4.8 years ago by ▴ 180
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0
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2.2k
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Comment: C: Error with gff file while building snpeff database
5.0 years ago by kristina.mahan ▴ 180
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1
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2.2k
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Comment: C: Error with gff file while building snpeff database
5.0 years ago by kristina.mahan ▴ 180
0
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1
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2.2k
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Comment: C: Error with gff file while building snpeff database
5.0 years ago by kristina.mahan ▴ 180
0
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6
replies
2.2k
views
Error with gff file while building snpeff database
gff java snpeff
updated 2.1 years ago by 45k • written 5.0 years ago by ▴ 180
2
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9
replies
3.6k
views
Getting a gff file from NCBI
gff ncbi
updated 5.0 years ago by ▴ 160 • written 5.0 years ago by ▴ 180
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0
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3.6k
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Comment: C: Getting a gff file from NCBI
5.0 years ago by kristina.mahan ▴ 180
0
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2
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3.6k
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Comment: C: Getting a gff file from NCBI
5.0 years ago by kristina.mahan ▴ 180
0
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1
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3.6k
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Comment: C: Getting a gff file from NCBI
5.0 years ago by kristina.mahan ▴ 180
1
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3
replies
1.6k
views
How to reduce Quast stats being based on "contigs of size > 100000 bp"
quast
updated 2.1 years ago by 45k • written 5.2 years ago by ▴ 180
0
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0
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1.7k
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Comment: C: Blobtools output files
5.1 years ago by kristina.mahan ▴ 180
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0
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3.4k
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Comment: C: Distinguishing sequencing reads as prokaryotic or eukaryotic without a reference
5.1 years ago by kristina.mahan ▴ 180
0
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2
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1.7k
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Blobtools output files
blobtools
updated 2.1 years ago by 45k • written 5.1 years ago by ▴ 180
0
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1
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1.7k
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Comment: A: Blobtools output files
5.1 years ago by kristina.mahan ▴ 180
0
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1
reply
1.3k
views
How to use gff file of old annotation to annotate new assembly
chloroplast gff
updated 2.1 years ago by 45k • written 5.1 years ago by ▴ 180
0
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1
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1.6k
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Comment: C: Illumina reads mapped back onto contigs have gaps
updated 5.1 years ago by 16k • written 5.1 years ago by ▴ 180
0
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6
replies
1.6k
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Illumina reads mapped back onto contigs have gaps
illumina
updated 2.1 years ago by 45k • written 5.1 years ago by ▴ 180
0
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1
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1.6k
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Comment: A: Illumina reads mapped back onto contigs have gaps
5.1 years ago by kristina.mahan ▴ 180
0
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0
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1.6k
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Comment: C: Illumina reads mapped back onto contigs have gaps
5.1 years ago by kristina.mahan ▴ 180
0
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1
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1.6k
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Comment: C: How to reduce Quast stats being based on "contigs of size > 100000 bp"
5.2 years ago by kristina.mahan ▴ 180
3
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0
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8.2k
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Answer: A: k-mer finding and counting
5.3 years ago by kristina.mahan ▴ 180
2
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1
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2.6k
views
How can you determine ploidy of a genome?
ploidy kmer genomescope jellyfish
updated 5.3 years ago by 35k • written 5.3 years ago by ▴ 180
0
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1
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1.3k
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BBnorm not outputting txt files when trying to determine ploidy on pb fastq.gz reads
kmer khist bbnorm bbmap ploidy
updated 5.3 years ago by 154k • written 5.3 years ago by ▴ 180
2
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0
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87k
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Answer: A: BAM/SAM to FASTA conversion
5.3 years ago by kristina.mahan ▴ 180
1
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1
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1.4k
views
How to remove circular contigs from assembly.fasta
de-novo-genome-assembly ngs
updated 2.1 years ago by 45k • written 5.3 years ago by ▴ 180
1
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0
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1.5k
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Comment: C: 18S sequence not matching 18S sequence in assembly
5.3 years ago by kristina.mahan ▴ 180
0
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0
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1.5k
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Comment: C: 18S sequence not matching 18S sequence in assembly
5.3 years ago by kristina.mahan ▴ 180
0
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1
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1.5k
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Comment: C: 18S sequence not matching 18S sequence in assembly
5.3 years ago by kristina.mahan ▴ 180
0
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0
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1.5k
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Comment: C: 18S sequence not matching 18S sequence in assembly
5.3 years ago by kristina.mahan ▴ 180
1
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1
reply
2.2k
views
How to extract a range of nucleotides from a fasta file
fasta
updated 2.1 years ago by 45k • written 5.3 years ago by ▴ 180
1
vote
6
replies
1.5k
views
18S sequence not matching 18S sequence in assembly
18S BLAST
updated 2.1 years ago by 45k • written 5.3 years ago by ▴ 180
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