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4
votes
3
replies
1.0k
views
How to download a genome assembly from the NCBI website?
genome
updated 18 months ago by 141k • written 18 months ago by ▴ 410
7
votes
10
replies
6.3k
views
Running multiQC on more than one file Log.final.out from STAR
multiqc star
updated 22 months ago by • 0 • written 7.5 years ago by ▴ 410
69
votes
17
replies
39k
views
12 follow
Transform a GTF file into a data frame in R
R RNA-Seq GTF
updated 14 months ago by 43k • written 6.6 years ago by ▴ 410
1
vote
4
replies
3.3k
views
How can I get a rdotplot file in lastz?
lastz r rdotplot dotplot genomic alignment
updated 3.8 years ago by 20 • written 6.7 years ago by ▴ 410
4
votes
1
reply
3.9k
views
How can I input a BAM file to the samtools mpileup command without using a text file?
samtools mpileup bam variant calling
updated 4.0 years ago by 20 • written 7.1 years ago by ▴ 410
2
votes
1
reply
1.3k
views
pacbio db and las files
db pacbio las next-gen
updated 13 months ago by 43k • written 6.9 years ago by ▴ 410
8
votes
7
replies
6.8k
views
How to rename chromosome names in GTF file?
GTF FASTA annotation genome
updated 5.6 years ago by 20 • written 6.6 years ago by ▴ 410
0
votes
0
replies
2.7k
views
Using the align() function of the Rsubread package; error: unrecognized option `--gtfFeature'
rsubread subread ngs next-gen seq alignment
updated 5.7 years ago by 43k • written 7.0 years ago by ▴ 410
8
votes
8
replies
4.0k
views
bwa mem misaligns my contigs to the reference by a few bases
bwa bwt bwa mem contig alignment
updated 5.8 years ago by 20 • written 6.8 years ago by ▴ 410
4
votes
4
replies
2.8k
views
Is there an R function that transforms a decimal SAM FLAG into a list of strings?
R SAM FLAG alignment format bam
updated 5.9 years ago by ▴ 10 • written 6.6 years ago by ▴ 410
5
votes
16
replies
7.9k
views
Problem with topGO: GO term enrichment analysis
go topgo bioconductor r error
updated 6.3 years ago by ▴ 10 • written 6.7 years ago by ▴ 410
0
votes
2
replies
2.9k
views
Problem installing quiver
quiver pacbio polishing arrow
updated 6.6 years ago by • 0 • written 6.8 years ago by ▴ 410
3
votes
1
reply
5.5k
views
Import the quality scores from a FASTQ file in Python 3 Biopython
python3 fastq biopython quality fasta
updated 6.6 years ago by 5.8k • written 6.6 years ago by ▴ 410
1
vote
2
replies
2.2k
views
Mauve, meaning of coulours and red bars and green lines
mauve alignment colour genomes
6.6 years ago by biomagician ▴ 410
0
votes
0
replies
1.6k
views
Difference between unlocalized and unplaced fragments
chromosomer scaffolding scaffold contig
6.7 years ago by biomagician ▴ 410
5
votes
3
replies
3.1k
views
Blastn error, database creation problem, BLAST
blast blastn database makeblastdb
updated 6.7 years ago by 35k • written 6.7 years ago by ▴ 410
9
votes
10
replies
4.4k
views
Problem installing Rgraphviz in R
graphviz rgraphviz bioconductor r plot
updated 6.7 years ago by 35k • written 6.7 years ago by ▴ 410
3
votes
5
replies
3.3k
views
Tool to analysis GO term enrichment in C. elegans
enrichment c.elegans r go
updated 16 months ago by 43k • written 6.7 years ago by ▴ 410
0
votes
1
reply
1.7k
views
Problem running chromosomer: error
chromosomer scaffolding
6.7 years ago by biomagician ▴ 410
2
votes
4
replies
3.3k
views
Problem using biomaRt
biomart bioconductor ensembl r error
6.7 years ago by biomagician ▴ 410
1
vote
3
replies
3.2k
views
data set geneList not found, problem in the topGO tutorial
go functional genomics bioconductor ALL topgo
6.7 years ago by biomagician ▴ 410
1
vote
5
replies
1.6k
views
how can I output the merged.gtf of cuffmerge in another folder ?
cuffmerge cufflinks gtf alignment assembly
6.7 years ago by biomagician ▴ 410
7
votes
13
replies
2.0k
views
Error with hera not finding the index
hera index error
updated 6.7 years ago by ▴ 80 • written 6.7 years ago by ▴ 410
4
votes
2
replies
1.5k
views
Error with hera
hera
updated 6.7 years ago by 47k • written 6.7 years ago by ▴ 410
1
vote
5
replies
2.2k
views
igv_plotter error, I cannot run igv_plotter on my BAM file, RuntimeError: Xvfb did not start
visualisation bam igv_plotter igv
updated 13 months ago by 43k • written 6.8 years ago by ▴ 410
0
votes
1
reply
1.4k
views
Problem installing multibreak-SV
install multibreak-sv SV pacbio
updated 6.8 years ago by • 0 • written 6.9 years ago by ▴ 410
2
votes
3
replies
1.6k
views
dedupe.sh from bbmap excludes contigs with insufficient overlap
dedupe bbmap contig assembly
6.8 years ago by biomagician ▴ 410
0
votes
1
reply
1.9k
views
dbsnp file for C. elegans
variation-file c.elegans dbsnp gatk
updated 13 months ago by 43k • written 6.8 years ago by ▴ 410
3
votes
1
reply
1.7k
views
Rsamtools and BAM file discordance
igv rsamtools samtools bam reads
updated 6.8 years ago by 104k • written 6.8 years ago by ▴ 410
6
votes
13
replies
3.0k
views
LASTZ does not accept/like "-" (dash) in Fasta file
lastz fasta alignment
6.8 years ago by biomagician ▴ 410
2
votes
2
replies
1.2k
views
Problem installing gasv
gasv gasvpro install structural variants SV
updated 6.9 years ago by 35k • written 6.9 years ago by ▴ 410
0
votes
1
reply
2.4k
views
Problem installing mummer
install mummer alignment nucmer
updated 6.9 years ago by 20 • written 6.9 years ago by ▴ 410
3
votes
5
replies
3.0k
views
Can't find show-aligns in mummer
mummer nucmer show-aligns allignment
updated 6.9 years ago by 35k • written 6.9 years ago by ▴ 410
1
vote
1
reply
2.0k
views
Can I improve my de novo assembly with a reference genome?
de novo assembly pacbio genome reference
6.9 years ago by biomagician ▴ 410
1
vote
3
replies
1.2k
views
Error in BLASR 'name in reference not unique'
blasr pacbio mapping error alignment
6.9 years ago by biomagician ▴ 410
4
votes
6
replies
5.6k
views
Canu: failed with exit code 134
canu pacbio failed exit code 134 genome assembly
6.9 years ago by biomagician ▴ 410
0
votes
3
replies
3.2k
views
Read metadata from a pacbio bam file
bam pacbio rsamtools sam R
6.9 years ago by biomagician ▴ 410
5
votes
25
replies
6.3k
views
Can I open a BAM file without a header in Rsamtools?
rsamtools bam scanBam samtools sequencing
6.9 years ago by biomagician ▴ 410
0
votes
0
replies
958
views
dextract multi-threadding possible?
dextract pacbio dazzler sequencing thread
6.9 years ago by biomagician ▴ 410
0
votes
0
replies
1.5k
views
fasta2DB command from DAZZ_DB
pacbio fasta2DB dazzler sequencing assembly
6.9 years ago by biomagician ▴ 410
3
votes
6
replies
1.3k
views
How to install DASQV?
dasqv pacbio scrubbing install
updated 7.0 years ago by 35k • written 7.0 years ago by ▴ 410
3
votes
2
replies
4.7k
views
Install kraken on Mac OS
kraken install macos mac
7.0 years ago by biomagician ▴ 410
9
votes
6
replies
1.6k
views
How can I redirect R's output from the console to a file
rsubread redirection r output
updated 7.0 years ago by 47k • written 7.0 years ago by ▴ 410
32
votes
6
replies
30k
views
Can STAR work with compressed .gz FASTQ input?
star fastq compressed gz alignment
updated 7.1 years ago by 5.7k • written 7.1 years ago by ▴ 410
6
votes
6
replies
9.8k
views
How do I get the weights of genes used in PCA in DESeq2?
deseq2 pca gene list loadings
updated 7.2 years ago by 13k • written 7.2 years ago by ▴ 410
4
votes
5
replies
3.1k
views
Downloading data from Short Read Archive
sra short read archive
updated 7.2 years ago by 7.5k • written 7.2 years ago by ▴ 410
0
votes
1
reply
2.0k
views
Problem with R package QuasR: qAlign function does not work
quasr r rnaseq qalign
7.4 years ago by biomagician ▴ 410
9
votes
9
replies
6.7k
views
Problem installing STAR on Mac OSX
star aligner installation
updated 7.5 years ago by ★ 2.1k • written 7.5 years ago by ▴ 410
7
votes
6
replies
4.5k
views
samtools faidx redirection
samtools index indexing samtools faidx redirection
updated 7.5 years ago by 161k • written 7.5 years ago by ▴ 410
0
votes
0
replies
2.5k
views
Mapping between gene IDs and transcripts IDs in C. elegans
mapping biomart ensembl gene id transcript id
7.5 years ago by biomagician ▴ 410
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