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1.6k
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Comment:
Comment: Constructing a bread wheat pangenome graph using PGGB: per-chromosome vs. whole-
5 weeks ago by
Sony Nguyen
▴ 20
1
vote
3
replies
1.6k
views
Constructing a bread wheat pangenome graph using PGGB: per-chromosome vs. whole-genome approach and integration of assemblies from different sequenci…
pangenome
structural-variation
bread-wheat
PGGB
updated 5 weeks ago by
samuel.a.odonnell
▴ 640 • written 5 weeks ago by
Sony Nguyen
▴ 20
1
vote
8
replies
2.5k
views
Tools for Subsampling Paired-End Reads to 25X Coverage ?
paired-end
fastq
depth
sequencing
coverage
updated 11 months ago by
Mensur Dlakic
★ 30k • written 11 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
2.5k
views
Comment:
Comment: Tools for Subsampling Paired-End Reads to 25X Coverage ?
11 months ago by
Sony Nguyen
▴ 20
0
votes
0
replies
804
views
Comment:
Comment: linear pangenome for crops
11 months ago by
Sony Nguyen
▴ 20
0
votes
0
replies
3.4k
views
Comment:
Comment: The BUSCO assessment of the MAKER annotation results shows a low completeness
11 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
730
views
How to compare and complement the missing gene and feature in gff3 file base on available gff3 reference ?
gff3
IRGSP1.0
MAKER
updated 12 months ago by
lieven.sterck
16k • written 12 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
3.4k
views
Comment:
Comment: The BUSCO assessment of the MAKER annotation results shows a low completeness
12 months ago by
Sony Nguyen
▴ 20
0
votes
0
replies
1.5k
views
Comment:
Comment: How to filter and keep longest isoform per gene in gff3 file ?
12 months ago by
Sony Nguyen
▴ 20
3
votes
3
replies
1.5k
views
How to filter and keep longest isoform per gene in gff3 file ?
gff
isoform
maker
annotation
12 months ago by
Sony Nguyen
▴ 20
0
votes
0
replies
458
views
How to extract the missing feature ( gene, CDS, ... when compare 2 gff3 file ?
gff3
compare
MAKER
annotation
RAP-DB
13 months ago by
Sony Nguyen
▴ 20
0
votes
0
replies
1.1k
views
Comment:
Comment: BUSCO did not find any match. Retraining did not complete correctly. BUSCO analy
16 months ago by
Sony Nguyen
▴ 20
0
votes
2
replies
1.1k
views
BUSCO did not find any match. Retraining did not complete correctly. BUSCO analysis failed!
Augustus
pipeline
MAKER
annotation
BUSCO
updated 16 months ago by
GenoMax
154k • written 16 months ago by
Sony Nguyen
▴ 20
0
votes
0
replies
965
views
ERROR with Maker annotation: The assumed RepeatMasker installation directory /opt/home/sony/miniconda3/envs/MAKER2/share/RepeatMasker does not ap…
RepeatMasker.
MAKER.
annotation.
18 months ago by
Sony Nguyen
▴ 20
1
vote
2
replies
779
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 18 months ago by
Ram
45k • written 18 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
1.3k
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 19 months ago by
GenoMax
154k • written 19 months ago by
Sony Nguyen
▴ 20
2
votes
4
replies
1.9k
views
Which command ro run MAKER pipeline for gene annotation ?
run.
command
to
MAKERpipeline.
updated 19 months ago by
GenoMax
154k • written 19 months ago by
Sony Nguyen
▴ 20
0
votes
2
replies
1.9k
views
Comment:
Comment: Which command ro run MAKER pipeline for gene annotation ?
19 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
1.7k
views
Comment:
Comment: How to download large-scale cDNA sequences from NCBI effectively ?
19 months ago by
Sony Nguyen
▴ 20
3
votes
4
replies
1.7k
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI.
cDNA
updated 19 months ago by
Pierre Lindenbaum
166k • written 19 months ago by
Sony Nguyen
▴ 20
0
votes
5
replies
1.5k
views
BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to solve this problem ?
duplicate
BUSCO.
updated 20 months ago by
GenoMax
154k • written 20 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
1.5k
views
Comment:
Comment: BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to
20 months ago by
Sony Nguyen
▴ 20
0
votes
0
replies
1.5k
views
Comment:
Comment: BUSCO analysis failed due to Duplicate of sequence in Input genome fasta. How to
20 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
773
views
How to perform GO enrichment analysis for assembled sequence ?
GO-enrichment
Gene-Ontology
updated 20 months ago by
Ram
45k • written 20 months ago by
Sony Nguyen
▴ 20
1
vote
3
replies
1.2k
views
How to validate the assembly completeness of unaligned reads ?
MaSuRCA
SPAdes
updated 20 months ago by
GenoMax
154k • written 20 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
1.2k
views
Comment:
Comment: How to validate the assembly completeness of unaligned reads ?
20 months ago by
Sony Nguyen
▴ 20
0
votes
0
replies
492
views
compare the assembler MaSuRCA and SPAdes for assembly unmapped reads
SPAdes
unmapped_reads.
assembly.
MaSuRCA.
20 months ago by
Sony Nguyen
▴ 20
2
votes
3
replies
1.3k
views
How to download all expressed sequence tags (ESTs) for particular species from NCBI using command ?
NCBI
EST
updated 21 months ago by
GenoMax
154k • written 21 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
1.3k
views
Comment:
Comment: How to download all expressed sequence tags (ESTs) for particular species from N
21 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
733
views
Validate the assembly of unmapped reads by remapping the original reads back to the assembled sequence
unmapped_reads.
assembly.
Paired-end_reads
updated 21 months ago by
GenoMax
154k • written 21 months ago by
Sony Nguyen
▴ 20
1
vote
5
replies
1.5k
views
How to calculate insert size and Stdev of insert file for Configure file of MaSuRCA assembly ?
MaSuRCA
insert-size
assembly
updated 21 months ago by
Ram
45k • written 21 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
1.5k
views
Comment:
Comment: How to calculate insert size and Stdev of insert file for Configure file of MaS
21 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
1.5k
views
Comment:
Comment: How to calculate insert size and Stdev of insert file for Configure file of MaS
updated 21 months ago by
GenoMax
154k • written 21 months ago by
Sony Nguyen
▴ 20
0
votes
0
replies
1.3k
views
Comment:
Comment: How to assess the quality of the assembly of unmapped reads ?
22 months ago by
Sony Nguyen
▴ 20
0
votes
0
replies
1.3k
views
Comment:
Comment: How to assess the quality of the assembly of unmapped reads ?
22 months ago by
Sony Nguyen
▴ 20
1
vote
0
replies
1.3k
views
Comment:
Comment: How to assess the quality of the assembly of unmapped reads ?
22 months ago by
Sony Nguyen
▴ 20
3
votes
5
replies
1.3k
views
How to assess the quality of the assembly of unmapped reads ?
Pangenome
Iterative-assembly
22 months ago by
Sony Nguyen
▴ 20
8
votes
3
replies
1.5k
views
How to construct a blast database for non-green plant species and fungi
blast
updated 22 months ago by
GenoMax
154k • written 22 months ago by
Sony Nguyen
▴ 20
8
votes
12
replies
4.5k
views
download BLAST NCBI nt database
blast
nt
updated 22 months ago by
PeterC_NCBI
▴ 520 • written 23 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
4.5k
views
Comment:
Comment: download BLAST NCBI nt database
22 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
4.5k
views
Comment:
Comment: download BLAST NCBI nt database
23 months ago by
Sony Nguyen
▴ 20
0
votes
1
reply
4.5k
views
Comment:
Comment: download BLAST NCBI nt database
23 months ago by
Sony Nguyen
▴ 20
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