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Bowtie2 reads alignment question
bowtie2 written 1 day ago by afli • 20 • updated 1 day ago by RamRS ♦ 17k
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1
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11k
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1
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Bowtie2 (ERR): bowtie2-align exited with value 1
bowtie2 alignment chip-seq written 2.6 years ago by s-root • 0 • updated 1 day ago by RamRS ♦ 17k
2
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1
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85
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1
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hisat2 / bowtie: read has more quality values than read characters
bowtie2 hisat2 bowtie hisat written 5 days ago by juan.crescente • 20
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68
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Bowtie2: trying to implement position specific scoring options?
bowtie2 alignment score bowtie srna written 5 days ago by brismiller • 10
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1
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755
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1
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bowtie2 filter for maximum alignment score
bowtie2 alignment written 20 months ago by rishi • 10 • updated 12 days ago by Biostar ♦♦ 20
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96
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calculating sequencing coverage for metagenome samples
illumina-hi-seq metagenomics sam bowtie2 written 13 days ago by mossigstamboulian • 30
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1
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127
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1
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sam file not showing multi mapped reads
bowtie2 sam written 14 days ago by mossigstamboulian • 30 • updated 13 days ago by RamRS ♦ 17k
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1
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Should --very-sensitive be combined with -no-1mm-upfront?
bowtie2 bowtie written 26 days ago by Lucy • 0 • updated 26 days ago by Devon Ryan ♦ 84k
2
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1
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132
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1
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Does Bowtie2 index use haplotypes and patches? and is the reference genome of Bowtie2 from UCSC or ensembl?
haplotypes bowtie2 chip-seq scaffolds ensembl written 7 weeks ago by salamandra • 170 • updated 7 weeks ago by Devon Ryan ♦ 84k
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1
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110
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1
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What is chr EBV in human sam file?
bowtie2 sam written 7 weeks ago by salamandra • 170 • updated 7 weeks ago by genomax ♦ 55k
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117
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Low coverage for bases near the end of target reference sequence
bowtie2 alignment sequencing written 7 weeks ago by kspata • 30
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4
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872
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5 follow
4
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Mapping contigs & scaffolds to ref genome?
assembly mapping bowtie2 written 11 months ago by YOUSEUFS • 10 • updated 8 weeks ago by h.mon ♦ 19k
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253
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problem with bowtie2 allignment
bowtie2 rna-seq written 10 weeks ago by arshil • 0 • updated 9 weeks ago by Biostar ♦♦ 20
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104
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bowtie2 paired end read alignment yieldsscaffold information for unmapped reads
bowtie2 unmapped tlen read alignment written 4 months ago by al.bodrug • 50 • updated 10 weeks ago by Biostar ♦♦ 20
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1
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157
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1
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Doubt regarding Reference genome alignment
bowtie2 next-gen alignment assembly written 11 weeks ago by bic • 0 • updated 11 weeks ago by pbpanigrahi • 170
2
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1
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203
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1
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bowtie2 paired end insertion length
bowtie2 ngs alignment paired end written 3 months ago by jesselee516 • 70 • updated 3 months ago by d-cameron • 1.9k
5
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1
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199
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1
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How to extract aligned exactly 1 time in Single end read?
bowtie2 alignment bwa written 3 months ago by star • 60 • updated 3 months ago by zx8754 ♦ 5.0k
4
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148
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no exact read?
R alignment chip-seq bwa bowtie2 written 3 months ago by star • 60
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268
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bowtie2-build index files missing
bowtie2 bowtie-build mapping bowtie2-build written 3 months ago by juan.crescente • 20
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279
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0
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bowtie2 unmapped reads
bowtie2 rna-seq assembly written 3 months ago by Sjannie Lefevre • 30 • updated 3 months ago by Devon Ryan ♦ 84k
1
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1
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229
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1
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bowtie2 mapping error: core dumped
bowtie2 alignment rna-seq written 4 months ago by lvyhwind • 0 • updated 4 months ago by genomax ♦ 55k
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2
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376
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6 follow
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Calculate Mapping Rate for an alignment to each sequence of a multi-fasta reference
flagstat samtools rna-seq mapping rate bowtie2 written 4 months ago by kspata • 30 • updated 4 months ago by h.mon ♦ 19k
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1
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193
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1
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Creating a Bowtie2 Index for S.Purpuratus to use in Galaxy
bowtie2 galaxy reference genome bowtie alignment written 4 months ago by alice_pieplow • 0 • updated 4 months ago by genomax ♦ 55k
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178
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metagenomic assembly coverage, for multiple samples
bowtie2 metagenomics samtools coverage mpileup written 4 months ago by willnotburn • 40
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158
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Low Mapping/Alignment rates with bowtie2 in mouse reduced genome
bowtie2 4cseq mapping libraryoffragments mm10 written 5 months ago by dzisis1986 • 20
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254
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metaphlan2 unclassified contigs
bowtie2 metagenomics metaphlan written 7 months ago by srdjan.kasapovic • 0 • updated 5 months ago by Biostar ♦♦ 20
5
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2
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435
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6 follow
2
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Error in samtools view
samtools bash chip-seq bowtie2 written 5 months ago by Bella_p • 50 • updated 5 months ago by Pierre Lindenbaum ♦ 112k
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1
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385
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1
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bowtie2 alignment has 'Duplicated sequence'
bowtie2 alignment sam bowtie2-build written 6 months ago by rmash • 0
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1
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181
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1
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Bowtie2 mapping did not finish, can I still use the .sam file?
bowtie2 bowtie written 6 months ago by jon.brate • 190 • updated 6 months ago by WouterDeCoster ♦ 32k
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1
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270
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1
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alignment score and other values for the whole paired-end alignment (with overlap)
bowtie2 paired-end alignment sam scores written 6 months ago by shim • 10 • updated 6 months ago by Devon Ryan ♦ 84k
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