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1
vote
9
replies
1.5k
views
blast retrieves "N/A" for taxonomic data
blast blastn
updated 8 weeks ago by • 0 • written 3.4 years ago by ▴ 50
0
votes
4
replies
447
views
Retrieving matched search terms when using NCBI's API
NCBI API
3 months ago by langziv ▴ 50
2
votes
2
replies
539
views
RAST annotation of RNA-seq transcriptome results in some genes appearing more than once
R RNA-seq
updated 6 months ago by ★ 2.5k • written 6 months ago by ▴ 50
0
votes
4
replies
750
views
Error when trying to create a heatmap with DESeq2
R heatmaps RNA-seq DESeq2
updated 6 months ago by 43k • written 6 months ago by ▴ 50
0
votes
20
replies
1.6k
views
Rockhoppper - Suspiciously low percentage of perfectly aligned reads
Rockhopper RNA-seq
6 months ago by langziv ▴ 50
0
votes
4
replies
749
views
Assessing Rockhopper's output
transcriptome Rockhopper RNA-seq de-novo-assembly
7 months ago by langziv ▴ 50
0
votes
2
replies
464
views
ptt and rnt files that were created from assembly rather than a genome
rockhopper genbank
7 months ago by langziv ▴ 50
1
vote
4
replies
605
views
Running Rockhopper from a command-line
rockhopper java
7 months ago by langziv ▴ 50
0
votes
13
replies
1.4k
views
Dealing with transcriptome sequences that are smaller than their respective genes
blastn Trinity Transcriptome De-novo-transcriptome-assembly RNA-seq
updated 6 months ago by 43k • written 7 months ago by ▴ 50
0
votes
0
replies
288
views
Associating between results obtained after running Trinity's run_DE_analysis.pl and genes
De-novo-transcriptome-assembly Trinity RNA-seq-analysis
8 months ago by langziv ▴ 50
3
votes
2
replies
554
views
Differential gene expression analysis after transcriptome assembly with SPAdes
SPAdes differential-expression transcriptome-assembly
updated 8 months ago by 100k • written 8 months ago by ▴ 50
2
votes
4
replies
574
views
Trinity output directory can be erased only with root privileges
trinity
updated 8 months ago by 43k • written 8 months ago by ▴ 50
1
vote
11
replies
1.2k
views
Quantification after transcriptome assembly with Trinity
De-novo-transcriptome-assembly Trinity RNA-seq-analysis
updated 7 months ago by 142k • written 8 months ago by ▴ 50
1
vote
1
reply
453
views
Quantifying genes' expression with Trinity
De-novo-transcriptome-assembly Trinity RNA-seq-analysis
updated 8 months ago by ★ 1.1k • written 8 months ago by ▴ 50
3
votes
5
replies
809
views
Creating a Trinity assembly
De-novo-transcriptome-assembly Trinity RNA-seq-analysis
updated 8 months ago by ★ 1.1k • written 8 months ago by ▴ 50
4
votes
2
replies
633
views
RNA-seq analysis with contigs instead of an assembled genome
rna-seq
updated 8 months ago by ★ 1.9k • written 8 months ago by ▴ 50
2
votes
6
replies
1.5k
views
Problems when trying to use ensembl-vep
ensembl ensembl-vep docker
updated 8 months ago by ★ 2.4k • written 9 months ago by ▴ 50
3
votes
12
replies
1.3k
views
Check if blastn gene matches are of entire genes or of parts of genes
blastx blastn bacteria
10 months ago by langziv ▴ 50
0
votes
0
replies
287
views
Tools for network enrichment analysis in bacteria
network-enrichment-analysis
11 months ago by langziv ▴ 50
0
votes
0
replies
406
views
Using RAST's API or as a command line tool‏‏
RAST command-line API
13 months ago by langziv ▴ 50
0
votes
1
reply
551
views
Get KEGG's functional annotation by KEGG organism ID and gene name
kegg kegg-api
updated 14 months ago by ★ 1.8k • written 14 months ago by ▴ 50
2
votes
3
replies
914
views
MAFFT freezes and nothing happens for over 2 hours
multiple-sequence-alignment maft
16 months ago by langziv ▴ 50
2
votes
2
replies
1.3k
views
Running blastn results in "Error: NCBI C++ Exception"
blastn blast command-line
updated 16 months ago by 142k • written 16 months ago by ▴ 50
3
votes
4
replies
825
views
Command-line blastn results in "Too many positional arguments" error
blastn command-line
updated 16 months ago by ▴ 360 • written 16 months ago by ▴ 50
7
votes
3
replies
1.9k
views
Using a Docker image with ensembl-vep
Linux ensembl-vep Docker
updated 16 months ago by ★ 2.1k • written 16 months ago by ▴ 50
0
votes
12
replies
1.7k
views
Splitting CRAM files
CRAM-files sequence-alignment
17 months ago by langziv ▴ 50
1
vote
5
replies
943
views
Getting information on CRAM files from headers inside the files
cram-file
updated 17 months ago by 142k • written 17 months ago by ▴ 50
2
votes
1
reply
452
views
Reference doesn't match the input's build in variant calling pipe line
variant-calling DeepVariant
updated 17 months ago by 43k • written 17 months ago by ▴ 50
1
vote
3
replies
1.1k
views
Getting "ValueError: NOT_FOUND: Could not open" when running the DeepVariant pipeline
variant-calling DeepVariant docker
updated 17 months ago by ▴ 610 • written 17 months ago by ▴ 50
1
vote
2
replies
648
views
The meaning of greter than character (>) in gene position in Genbank files
genbank
updated 2.2 years ago by 21k • written 2.2 years ago by ▴ 50
0
votes
0
replies
311
views
Getting a negative values when calculating gene expression
RNA-seq EDGE-pro gene-expression
2.2 years ago by langziv ▴ 50
0
votes
0
replies
389
views
Error when trying to use the R package BOG for GSEA and COG
RNA-seq R cluster-of-orthologous-genes bog Gene-Set-Enrichment-Analysis
2.3 years ago by langziv ▴ 50
3
votes
8
replies
1.9k
views
Getting genes' sequences by querying gene symbols/names
gene-sequence gene-id human gene-symbol
updated 2.4 years ago by ▴ 720 • written 2.5 years ago by ▴ 50
0
votes
5
replies
1.7k
views
API for retrieving genes' sequences from genes' symbols in a single call
gene-sequence linux API gene-symbol
updated 2.4 years ago by 35k • written 2.4 years ago by ▴ 50
2
votes
7
replies
2.9k
views
"Input file does not exist" error message when using the Windows version of ensembl-vep with Docker‏‏‏‏
vep emsembl docker ensembl-vep
2.4 years ago by langziv ▴ 50
0
votes
1
reply
1.2k
views
Running a Linux command for "Ubuntu on Windows" with WSL from a python script
ensembl-vep windows-subsystem-for-linux wsl python ubuntu
updated 2.4 years ago by • 0 • written 2.4 years ago by ▴ 50
0
votes
5
replies
1.3k
views
Error when trying to use Ensembl virtual machine
vep ensembl ensemble-virtual-machine
2.4 years ago by langziv ▴ 50
1
vote
2
replies
1.2k
views
Many TLENs in a SAM file seem much too big
NGS SAM comperative-genomics alignment
updated 2.8 years ago by ★ 2.9k • written 2.8 years ago by ▴ 50
3
votes
1
reply
596
views
Annotating an assembly according to alignment against a reference genome
genbank annotation alignment
updated 2.8 years ago by ★ 27k • written 2.8 years ago by ▴ 50
2
votes
9
replies
2.1k
views
Getting command line blastn results for the complementary strand
blast command-line blastn
updated 2.8 years ago by 15k • written 2.8 years ago by ▴ 50
2
votes
4
replies
1.2k
views
BLAST Database error: No alias or index file found for nucleotide database
blast blastx
updated 2.8 years ago by 142k • written 2.8 years ago by ▴ 50
1
vote
4
replies
1.2k
views
Finding the sex of an individual from an NGS output's alignment to a reference
coverage NGS samtools
2.8 years ago by langziv ▴ 50
1
vote
8
replies
1.2k
views
Unexpected blastx results
blast blastx
2.5 years ago by langziv ▴ 50
2
votes
2
replies
1.1k
views
Using DAVID Web Service to classify genes into functional groups
DAVID-Web-Service david
2.9 years ago by langziv ▴ 50
4
votes
4
replies
1.0k
views
Accessing blast nt database
database blast
2.9 years ago by langziv ▴ 50
0
votes
2
replies
479
views
blastn returns multiple identical lines
blast blastn
2.9 years ago by langziv ▴ 50
3
votes
7
replies
1.6k
views
BLASTX script doesn't print results and never ends
blastx command-line
updated 2.9 years ago by 43k • written 3.0 years ago by ▴ 50
7
votes
12
replies
1.7k
views
Failing to run tblastn
tblstn blast
updated 3.0 years ago by 142k • written 3.0 years ago by ▴ 50
1
vote
6
replies
2.2k
views
Dealing with chimeric assembly contigs
comperative-genomics assembly chimera-contig
updated 3.1 years ago by ▴ 520 • written 3.1 years ago by ▴ 50
1
vote
4
replies
1.6k
views
BLAST results shows partial matches
blast BLAST assembly
3.1 years ago by langziv ▴ 50
63 results • Page 1 of 2
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