Limit : all time
all time today this week this month this year
50 results • Page 1 of 1
Sort: Rank
Rank Views Votes Replies
Showing top results for tag: BWA • reset
9
votes
7
replies
5.4k
views
Aligning MiSeq targeted amplicons (ultra-deep sequencing)
MiSeq Targeted Sequencing Alignment BWA ultra-deep
updated 7 days ago by • 0 • written 6.9 years ago by ▴ 130
0
votes
0
replies
124
views
bamdst gives error "EOF marker is absent. The input is probably truncated."
bwa samtools bamdst
9 days ago by shpak.max • 0
2
votes
2
replies
162
views
BWA error: [bwa_idx_build] fail to open file 'ref.fa' : No such file or directory
BWA
updated 10 days ago by 10k • written 10 days ago by • 0
44
votes
2
replies
32k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa tutorial Tutorial
updated 11 days ago by • 0 • written 9.3 years ago by ▴ 530
1
vote
3
replies
178
views
Troubleshooting Missing_Read_Group and Mismatch_Flag_Mate Errors
Picard BWA
updated 10 days ago by 104k • written 13 days ago by • 0
0
votes
2
replies
131
views
transfer parameter to reader group in bwa mem command
bwa
13 days ago by Chenfei Zheng ▴ 60
2
votes
3
replies
162
views
Contigs and scaffold in reference genome
BWA Ensembl Genome Reference HiSat NCBI
updated 15 days ago by 104k • written 15 days ago by ▴ 380
0
votes
0
replies
61
views
Co-binning with Metabat2, how do I map my reads with BWA?
Metabat2 Co-binning BWA
20 days ago by howla1ke • 0
0
votes
2
replies
129
views
Rainbow-fied bams in igv
alignment bwa gatk
21 days ago by Siddharth • 0
1
vote
2
replies
141
views
SortSam Error after BWA alignment
alignment mappingquality picard sortsam bwa
15 days ago by loy_loy • 0
2
votes
2
replies
253
views
Remove A List of Sequences from the MSA File
BAMtools SAMtools Multiple BWA BCFtools Alignment Sequence
24 days ago by Tastulek • 0
2
votes
3
replies
159
views
Why split fastq files?
fastq alignments ngs bwa
updated 4 weeks ago by 104k • written 4 weeks ago by • 0
2
votes
2
replies
148
views
BWA aln, according to GDC DNA Seq Analysis Pipeline
scores BWA quality GDC Alignment
updated 4 weeks ago by ▴ 420 • written 5 weeks ago by • 0
0
votes
1
reply
99
views
Buffer Error with bwa index
hg19 index bwa
updated 5 weeks ago by 137k • written 5 weeks ago by ▴ 150
1
vote
4
replies
184
views
What is the best short reader to very large reference fasta?
mapping alignment fastq bowtie2 bwa read
6 weeks ago by O.rka ▴ 320
36
votes
8
replies
41k
views
10 follow
Adding Read Groups To Bam Files
bam gatk samtools bwa
updated 6 weeks ago by 10k • written 9.1 years ago by 11k
1
vote
1
reply
190
views
BWA alignment score calculation
score SAM BWA alignment
updated 7 weeks ago by ★ 1.7k • written 7 weeks ago by ▴ 10
6
votes
10
replies
456
views
Gaps in alignment
NGS mem bwa alignment
7 weeks ago by mikegrootde ▴ 20
0
votes
0
replies
125
views
Can you generate a mappability mask with STAR (or another splice-aware aligner)?
STAR mappability SNPable bwa
9 weeks ago by mercerf93 • 0
2
votes
2
replies
219
views
Stop BWA mem trimming
fasta2sam BWA BWA-mem alignment
updated 5 weeks ago by 34k • written 9 weeks ago by • 0
2
votes
5
replies
320
views
alignement and Variant calling with BWA and samtools
variantcalling BWA samtools
updated 9 weeks ago by 13k • written 12 weeks ago by ▴ 10
2
votes
2
replies
191
views
paired reads have different names
BWA
updated 12 weeks ago by 104k • written 12 weeks ago by ▴ 10
0
votes
2
replies
229
views
why do the header of bwa mapping sam files show [M::main_mem]
shell bwa genome chip mapping
3 months ago by szp770 ▴ 10
7
votes
7
replies
444
views
Inconsistency between alignment rates of BWA-mem and bowtie2
Bowtie NGS BWA
updated 3 months ago by 89k • written 3 months ago by • 0
1
vote
3
replies
385
views
BWA mem or samtools have any parameter to filter the mismatch reads？
mapping samtools reads BWA
3 months ago by Damon_Wan • 0
0
votes
0
replies
131
views
The effect of heterozygosity on genome alignment
heterozigosity alignment bwa sequence
3 months ago by Iseez • 0
2
votes
8
replies
552
views
BWA mapping quality 0 for all reads
mapping mapping_quality bwa
updated 3 months ago by 89k • written 3 months ago by • 0
4
votes
7
replies
594
views
How are BWA/bowtie/etc indices built for multiple fasta entries?
index fasta mapping BWA bowtie
3 months ago by maxrwjones898 ▴ 20
0
votes
0
replies
132
views
Resistome Analyzer Report
bwa metagenomic resistome
3 months ago by ylhyang • 0
0
votes
2
replies
239
views
Most stringent settings for bwa mem
alignment bwa dna
updated 3 months ago by 89k • written 3 months ago by ▴ 90
1
vote
5
replies
494
views
What is the most accurate short (ish) read aligner?
aligner sequencing bwa minimap2
updated 3 months ago by 89k • written 4 months ago by ▴ 90
0
votes
4
replies
403
views
[E::bwa_idx_load_from_disk] fail to locate the index files
bwa
updated 4 months ago by 104k • written 4 months ago by • 0
2
votes
1
reply
278
views
BWA-MEM or BWA-ALN + BWA-SAMSE for MGI sequencing
bwa ali sequencing
updated 4 months ago by 52k • written 4 months ago by • 0
0
votes
0
replies
172
views
Total number of trimmed reads less than number of mapped reads
alignment next-gen sequence SAMtools BWA
4 months ago by kspata ▴ 70
1
vote
4
replies
248
views
How to optimized the alignment with bwa mem
genome bwa alignment
5 months ago by quentin54520 • 0
0
votes
1
reply
200
views
Alignment Error in BWA: The sequence "lcl|" was not found
bwa DNA-Seq alignment
5 months ago by gt • 0
1
vote
8
replies
2.9k
views
[mem_sam_pe] paired reads have different names. Without -p
bwa alignment next-gen
updated 5 months ago by ★ 1.4k • written 3.4 years ago by ▴ 20
3
votes
5
replies
237
views
problem to aligning FASTQ through BWA aligner
genome BWA alignment
updated 5 months ago by ★ 1.6k • written 5 months ago by ▴ 140
2
votes
6
replies
248
views
reduce speed terminal command submission
terminal macos bwa
updated 5 months ago by 34k • written 5 months ago by ▴ 10
2
votes
6
replies
262
views
is "sequence Duplication levels" has bad effect on Alignment process?
bwa FastQC RNA-seq
updated 5 months ago by 52k • written 5 months ago by ▴ 140
7
votes
6
replies
258
views
what should be view inside of SAM file?
SAM BWA
updated 6 months ago by ★ 4.7k • written 6 months ago by ▴ 140
0
votes
7
replies
253
views
Riboseq - pairs unaligned to rRNA get mixed up
riboseq bwa
6 months ago by blur ▴ 190
2
votes
10
replies
1.3k
views
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 5 weeks ago by • 0 • written 7 months ago by ▴ 20
1
vote
2
replies
270
views
BWA aligner error: paired reads have different names
bwa
7 months ago by MAPK ★ 1.8k
0
votes
0
replies
251
views
CIRI2 not working properly with overlapping paired-end reads
RNA-Seq overlapping reads circrna ciri BWA
7 months ago by dario.d • 0
8
votes
6
replies
2.6k
views
Getting Index Error 12 When Attempting To Index A Genome With Bwa
bwa next-gen bioinformatics
updated 7 months ago by 20 • written 8.5 years ago by ▴ 10
1
vote
3
replies
334
views
Is it possible to convert bam files with different parameters?
BWA NGS WGS
updated 7 months ago by 52k • written 7 months ago by ▴ 20
1
vote
3
replies
395
views
Using paired-end date as single-end for mapping with bwa mem. Good, bad or ugly?
alignment bwa paired-end polishing Racon
updated 8 months ago by 104k • written 8 months ago by ▴ 10
0
votes
10
replies
307
views
Open files created with bwa
BWA
8 months ago by mostafarafiepour ▴ 130
0
votes
1
reply
322
views
bwa aln writing speed became very slow after being very fast. What is the pattern of output size?
alignment next-gen bwa
updated 8 months ago by ★ 2.3k • written 8 months ago by • 0
50 results • Page 1 of 1
Recent Votes
Answer: Using R in Conda
Comment: Why is WGS/WES depth of Y chromosome highly variable?
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Download list of all genes of genome build GRCh38.p0
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Recent Locations • All
Lugano, just now
Hyderabad India, just now
Australia, 1 minute ago
Thailand, 2 minutes ago
France, 2 minutes ago
Bergen, Norway, 3 minutes ago
Calcutta, India, 3 minutes ago
Recent Awards • All
Scholar to Papyrus ★ 1.2k
Teacher to Prakki Rama ★ 2.5k
Commentator to Devon Ryan 99k
Great Question to Woa ★ 2.8k
Supporter to Ömer An ▴ 230
Popular Question to pthom010 ▴ 10
Scholar to roy.granit ▴ 880
Recent Replies
Comment: Plot assigned / unassigned reads distance to 3'UTR by Pierre Lindenbaum 137k
what does `distances.bed` looks like please ?
Comment: Why is WGS/WES depth of Y chromosome highly variable? by German.M.Demidov ★ 2.3k
Correct - could be more frequent for aneuploidies https://www.nature.com/articles/s41586-020-2426-2
Comment: Why is WGS/WES depth of Y chromosome highly variable? by crisime ▴ 240
The paper you shared is detecting CHIP events (SNP/indel) in 18,4% of >90 year old people by looking at just 160 WES genes. So it does not…
Comment: How to plot/combine biological replicates on a genomic features plot for methyla by Papyrus ★ 1.2k
You can take the mean/average to pool the replicates, and it is OK. Nonetheless, you have another option which does not involve losing/pool…
Comment: Biopython SeqIO: AttributeError: 'str' object has no attribute 'id' by cpad0112 16k
`desired_proteins=seq` you are assigning only sequence here.
Comment: How to convert gene names to EC numbers? by lieven.sterck 12k
ok, it has been a while apparently :) it is a two-step procedure, first get the GO-labels from interpro and 'convert' those to EC numbers …
Answer: Biopython SeqIO: AttributeError: 'str' object has no attribute 'id' by Shred ▴ 380
You're passing the wrong object to `SeqIO.write`: it expects a `SeqRecord`, and instead it gets a `Seq` object. [documentation][1] Outp…
Comment: Tools for bulk RNA-seq celltype deconvolution by Papyrus ★ 1.2k
Thank you for the info, I'll be sure to check it out!
Comment: Why is WGS/WES depth of Y chromosome highly variable? by German.M.Demidov ★ 2.3k
It also depends which degree of mosaicism we'd check - I normally check anything happened in >20% of cells. Otherwise it becomes much more …
Comment: BLAST memory usage by reany • 0
How to cache the db into memory? Is there an operable method?
Comment: Reference file for base recalibration by priya.bmg • 0
I figured out that I have to create FASTA reference sequence dictionary file. For creating the dictionary file, the command GATK-Launch doe…
Comment: How to modify dot plot in MUMmer 3 for bacteria comparative genomics? by Manuela ▴ 30
As said in the question post:1. I do not understand how I can modify the gnuplot file since it is generated together with the plot; 2. the …
Comment: Strand specific quantification with strand-splitted BAM files by compuTE ▴ 60
Hi! Thank you so much for your answer! I really appreciate the tutorial you did about filtering alignments by strand :-) Yes, I understand …
Comment: collapsing pacbio reads into a single sequence by Sara ▴ 180
@genomax yes subreads.bam is the input for ccs tool.
Comment: Reference file for base recalibration by priya.bmg • 0
Is there problem with Java?. I tried renaming the file, still got the same error java.lang.IllegalArgumentException: File is not a sup…
Traffic: 2449 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6