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Showing top results for tag: assembly • reset
0
votes
0
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35
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Suggestions for Alternate Assembly Resources to Trinity
assembly trinity HPC
19 hours ago by kacollier • 0
3
votes
13
replies
698
views
6 follow
large number of contigs after assembly
Nanopore genome assembly wtdbg2 sequencing
updated 1 day ago by ★ 3.1k • written 14 days ago by ▴ 20
0
votes
2
replies
98
views
How can I get PHRED score?
novo PHRED Trinity de assembly RNAseq
updated 1 day ago by ▴ 480 • written 1 day ago by ▴ 30
4
votes
3
replies
150
views
What is the correct syntax for BioPythons SeqIO.parse()
assembly biopython
updated 9 hours ago by 7.3k • written 2 days ago by ▴ 50
0
votes
1
reply
96
views
N50 is too short in de novo assembly
assembly N50 genome
updated 4 days ago by 89k • written 4 days ago by • 0
2
votes
6
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343
views
6 follow
Extracting exons and transcripts from gff3/gtf
assembly gtf annotation gff3
2 days ago by mglasena ▴ 30
3
votes
6
replies
370
views
What are the rules for the basic statistic of de novo assembly in RNAseq?
Assembly Trinity RNAseq
6 days ago by Riku ▴ 30
0
votes
1
reply
105
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Has anyone here used the MAC tool for merging assemblies?
assembly WGS genomes
updated 9 days ago by 49k • written 9 days ago by • 0
2
votes
1
reply
141
views
Update SNP map
assembly update SNP map
updated 15 days ago by ▴ 600 • written 15 days ago by • 0
14
votes
23
replies
7.5k
views
13 follow
Where can I get ?or how can I make a mappability track for hg38 assembly
sequencing alignment Assembly sequence
8 days ago by manojkumar_bhosale ▴ 70
0
votes
10
replies
398
views
How to align fastq files against a reference assembly
assembly alignment bacterial hisat2
updated 14 days ago by ▴ 320 • written 18 days ago by • 0
0
votes
0
replies
66
views
distinguish between alleles and isoforms in a de novo assembly
assembly
20 days ago by utsafar ▴ 80
5
votes
2
replies
176
views
Hybrid assembly SPAdes (Ox. Nanopore + Illumina)
assembly hybrid SPAdes
updated 14 days ago by ★ 3.1k • written 21 days ago by ▴ 60
2
votes
6
replies
312
views
Assembly with repetitive regions
Flye Assembly Canu SPAdes
22 days ago by msrch • 0
2
votes
1
reply
186
views
Interpretation of .gfa
flye bandage assembly
4 weeks ago by Rox ★ 1.3k
1
vote
2
replies
165
views
Accuracy Assembly's contigs
NGS Assembly whole genome Velvet
4 weeks ago by askari.arezou94 ▴ 30
1
vote
2
replies
464
views
How to convert plink data from 38th assembly to 37
assembly SNP plink liftOver genome
updated 7 days ago by ▴ 30 • written 6 months ago by ▴ 220
1
vote
4
replies
654
views
Extract reads used for contigs assembly
assembly sequencing RNA-Seq
updated 5 weeks ago by 17k • written 2.5 years ago by • 0
0
votes
1
reply
163
views
How to find the co ordinates of long reads (simulated by Badreads) with respect to the reference genome
mapping Badreads reference genome assembly long reads
updated 5 weeks ago by 106k • written 5 weeks ago by ▴ 10
0
votes
2
replies
139
views
Map Entire Directory of Paired-End Reads at Once
bwa bowtie genomics assembly reads
updated 5 weeks ago by 33k • written 5 weeks ago by • 0
1
vote
5
replies
363
views
De novo genome assembly
De novo Assembly Genome Minimap2 Mother
updated 5 weeks ago by 106k • written 5 weeks ago by • 0
0
votes
3
replies
265
views
fastq-dump: command not found, what is wrong?
assembly toolkit genomics SRA
updated 5 weeks ago by ▴ 10 • written 5 weeks ago by • 0
5
votes
5
replies
373
views
6 follow
SPAdes did not assemble the genome completely
SPAdes FASTQ genome assembly FASTA
updated 6 weeks ago by ★ 13k • written 6 weeks ago by • 0
1
vote
5
replies
1.7k
views
FastUniq error - Error in open left fastq file site1_R1_P_qtrim.fq for read!
software error fastuniq assembly
updated 3.4 years ago by 106k • written 3.4 years ago by ▴ 30
0
votes
3
replies
277
views
Decoy sequence for human reference GRCh38 assembly
reference genome Decoy assembly Human
updated 6 weeks ago by ★ 1.0k • written 6 weeks ago by • 0
0
votes
5
replies
572
views
Removing specified range of bases from middle of the contigs and creating new sequences
Contigs Assembly fastafile
updated 6 weeks ago by 17k • written 6 weeks ago by ▴ 210
2
votes
2
replies
370
views
Will this de novo transcriptome assembly be useful in looking at RNAseq differential expression?
novo quality transcriptome de assembly
updated 6 weeks ago by ★ 1.5k • written 6 weeks ago by ▴ 140
1
vote
6
replies
310
views
How to group transcripts by "gene" from different transcript assemblies?
assembly trinity rnaspades transcript
updated 7 weeks ago by ▴ 490 • written 7 weeks ago by ▴ 350
1
vote
3
replies
656
views
SSPACE bowtie and bwa error
Assembly next-gen software error genome
updated 7 weeks ago by ▴ 10 • written 2.2 years ago by ▴ 60
1
vote
0
replies
110
views
Tool: BIRCH Bioinformatics System v3.80
alignment RNA-seq genome assembly sequence phylogeny
8 weeks ago by brian.fristensky ▴ 270
2
votes
3
replies
643
views
How to get GTF file of virus genome
genome gene assembly
updated 8 weeks ago by • 0 • written 15 months ago by ▴ 120
3
votes
5
replies
1.2k
views
Does Last aligner only outputs the mapped reads to a bam file ?
assembly alignment sequencing next-gen genome
updated 8 weeks ago by • 0 • written 3.1 years ago by ▴ 130
0
votes
0
replies
154
views
Job: Postdocs @ New York City: Long Reads Epigenomics, Metagenomics and Transcriptomics
epigenomics splicing assembly sequencing microbiome
9 weeks ago by fanggang ▴ 100
0
votes
1
reply
190
views
Generating a dotplot following ragtag scaffolding
ragtag dotplot mummerplot genome assembly
updated 9 weeks ago by ▴ 300 • written 9 weeks ago by • 0
0
votes
1
reply
164
views
HiSat2 and StringTie! -StringTie empty GTF file
transcript assembly hisat2 stringtie DNA
updated 9 weeks ago by 17k • written 9 weeks ago by • 0
3
votes
4
replies
367
views
Flye assembly, increased coverage results in decreased N50
Minion genome assembly flye sequencing
9 weeks ago by roger.huerlimann ▴ 10
0
votes
1
reply
158
views
reference-guided denovo assembly
next-gen denovo stringTie Assembly genome assembl reference-guided
updated 10 weeks ago by 106k • written 10 weeks ago by ▴ 30
7
votes
2
replies
4.5k
views
Trinity : How To Co-Assemble Different Samples (Tumor And Healthy)
trinity assembly transcriptome
updated 10 weeks ago by • 0 • written 9.6 years ago by 9.5k
3
votes
4
replies
403
views
sugestion nanopore assembly and illumina reads
nanopore assembly illumina
updated 9 weeks ago by ★ 1.7k • written 10 weeks ago by ▴ 70
1
vote
4
replies
245
views
Human de novo genome assembly resulting in bad quality assemblies
sga de human genome novo low coverage assembly
10 weeks ago by Jess • 0
1
vote
5
replies
2.3k
views
to extract fasta file from PDB and obtain the content of file only as protein sequence
alignment sequence assembly
updated 10 weeks ago by 106k • written 16 months ago by • 0
3
votes
4
replies
322
views
DENOVO ASSEMBLY
assembly NGS Assembly Denovo
updated 10 weeks ago by ★ 2.7k • written 10 weeks ago by ▴ 30
2
votes
2
replies
285
views
How much would it cost to do a de novo assembly (plus annotation) of a jellifish genome?
novo genome de assembly budgeting
24 days ago by ilante ▴ 30
0
votes
2
replies
159
views
Unicycler error not enough memory available
assembly unicycler memory
updated 10 weeks ago by ★ 13k • written 11 weeks ago by ▴ 60
1
vote
6
replies
564
views
Aligning PacBio hifiasm CCS to reference genome using pbmm2
assembly pbmm2 pacbio hifiasm
updated 11 weeks ago by ▴ 10 • written 4 months ago by • 0
1
vote
4
replies
405
views
How to curate the genome assemblies after polishing and scaffolding?
assembly genome
9 weeks ago by zzz • 0
0
votes
4
replies
312
views
how to merge two files in two columns using bash command lines
assembly fasta trinity
updated 12 weeks ago by ▴ 320 • written 12 weeks ago by ▴ 10
2
votes
3
replies
261
views
Assembly of three biological replicated metagenomics data
Assembly metagenomics analysis replicate statistics
updated 12 weeks ago by ★ 1.7k • written 12 weeks ago by • 0
0
votes
0
replies
123
views
Genome assembly
illumina bam genome vcf assembly
updated 12 weeks ago by 53k • written 12 weeks ago by • 0
1
vote
1
reply
252
views
How to extract the shortest and the longest isoform from Trinity.fasta file?
assembly fasta trinity
updated 12 weeks ago by ★ 1.7k • written 12 weeks ago by ▴ 10
50 results • Page 1 of 1
Recent Votes
Comment: Genozip: A new compression tool for FASTQ, BAM, VCF and more
Comment: How to remove Illumina TruSeq Index adapters reverse (R2 reads )
How can I draw this plot?
Interpreting output of BCFtools RoH
Answer: Is there any software that can use ATAC-seq to identify super enhancer
A: Alignment and mapping
Comment: Flat Volcano plot
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Recent Replies
Comment: How to remove Illumina TruSeq Index adapters reverse (R2 reads ) by GenoMax 106k
Can you post an example of what you are referring to? Normally trimming programs should check reverse complements of sequences they are loo…
Comment: Genozip: A new compression tool for FASTQ, BAM, VCF and more by matthew.pobox ▴ 10
This seems like a great tool which has been seriously overlooked. I've been testing it out and was able to reproduce the compression ra…
Comment: get read length from sra by Renesh ★ 2.0k
The suggested methods works. Here is another method using the [SRA toolkit][1] fastq-dump -X 1 -Z SRR5790106 | sed -n '2p' | awk '{ pr…
Comment: Primers trimming from Illumina paired-end reads by BBDuk software by GenoMax 106k
Following should work. Give it a try and let me know. bbduk.sh -Xmx2g in1=test_R1.fq in2=test_R2.fq out1=R1_trim.fq out2=R2_trim.fq li…
Answer: Database for Enhancers with Coordinates by Papyrus ★ 1.3k
Also check [EnhancerAtlas][1], apart from coordinates it provides predictions for enhancer-gene target interactions, which may be useful. …
Comment: How can I draw this plot? by gubrins ▴ 90
Heys, did you manage to plot it?
Comment: get read length from sra by GenoMax 106k
You will only get average length of reads (which may or may not be very useful) using [Entrezdirect][1]. $ esearch -db sra -query "SRR…
Comment: Interpreting output of BCFtools RoH by gubrins ▴ 90
Heys, did you manage in interpreting and visualizing the output? I'm in the same situation...
Comment: which tool can I use to detect CNVs? by brunobsouzaa ▴ 560
`cnvkit` and `ExomeDepth` are great tools for that. Also, both are pretty straightforward to use.
Comment: rsem-calculate-expression with STAR takes forever but without error by Fleur • 0
Thanks both! I will try :) :)
Comment: rsem-calculate-expression with STAR takes forever but without error by Fleur • 0
Ah yes, sounds similar to tmux which is what I'm using. That also makes sure that the job keeps running when you close the terminal. Thanks…
Comment: which tool can I use to detect CNVs? by patelk26 ▴ 250
You could try CNVkit. You can create a reference copy number profile without normal samples.
Answer: Is there any software that can use ATAC-seq to identify super enhancer by jared.andrews07 ★ 11k
The original paper actually used a collection of TFs + Mediator. ROSE was not designed for H3K27ac use, though both the authors and others …
Comment: get read length from sra by ATpoint 53k
https://www.biostars.org/p/115936/#115962
Comment: script to organize files by Galileo • 0
I found a solution: used dos2unix on the files that have '$'\r' at the end :)
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