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113
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From sam data, how do I tell from which fastq file each read came from?
bowtie2 sam read file origin parsing written 4 days ago by bitjunkie • 40
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2
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112
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2
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align spike in database
bowtie2 spike-in rna-seq fastqc written 5 days ago by mail4malla • 0 • updated 5 days ago by swbarnes2 ♦ 2.8k
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133
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bowtie2: user error or a bug?
unpaired bowtie2 multiple files written 6 days ago by bitjunkie • 40
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1
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117
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1
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Samtools flagstat unpaired reads
bowtie2 bam samtools written 6 days ago by rbronste • 120 • updated 6 days ago by Pierre Lindenbaum ♦ 96k
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1
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101
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1
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Bowtie2 parallelization on cluster
bowtie2 alignment written 7 days ago by rbronste • 120 • updated 7 days ago by erictleung • 80
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1.5k
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Hisat2 versus Bowtie2
bowtie2 exome-sequencing hisat2 written 14 months ago by nalpas.nicolas • 20 • updated 16 days ago by Biostar ♦♦ 20
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160
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bowtie2 - Can anybody explain the mismatches in the alignment if no mismatches are allowed in the seed?
bowtie2 alignment seeds bowtie mismatches written 27 days ago by shim • 0 • updated 16 days ago by Ram ♦ 12k
2
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1
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131
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1
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Recommended program for evaluating aligner sensitivity
bowtie2 stampy soap smalt bwa written 21 days ago by fiona.newberry • 50 • updated 21 days ago by mark.ziemann • 870
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131
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sorting bowtie2 results using samtools sort
bowtie2 samtools sort written 27 days ago by ggman • 40
4
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188
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Bowtie2 end-to-end alignment seems does not work for Fasta files?
software error bowtie2 alignment written 4 weeks ago by m.koohi.m • 60
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185
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Error message produced by bowtie2 (HiC-Pro)
bowtie2 hic-pro hichip alignment written 5 weeks ago by Gary • 380
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123
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Error with Bowtie 2
bowtie2 alignment written 6 weeks ago by valerie • 30
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135
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5 follow
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Using a bash loop script to map multiple samples in PBS
bowtie2 alignment pbs written 7 weeks ago by t86dan • 0 • updated 7 weeks ago by h.mon ♦ 7.4k
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1
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206
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7 follow
1
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Bowtie2/HISAT using single-end to generate FPKM???
bowtie2 fpkm hisat rna-seq rpkm written 8 weeks ago by jamieson.pierce • 10 • updated 8 weeks ago by Brian Bushnell ♦ 13k
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248
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Mapping miRNA with Bowtie & Bowtie2
bowtie2 mapping bowtie mirna written 10 weeks ago by gkuffel22 • 20
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1
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252
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1
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bowtie2-align died with signal 6 (ABRT) (core dumped)
genome mapping bowtie2 alignment written 11 weeks ago by micro32uvas • 0
2
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200
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Fistful of failures with Bowtie2 in Trinity
software error trinity rna-seq bowtie2 written 11 weeks ago by akijl • 20
1
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170
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which alignment tool is better to use to align genome on short reference sequence ~5000b.p
bowtie2 alignment bwa use written 11 weeks ago by bbb • 30
3
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1
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220
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1
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Error encountered using bowtie2 on Illumina fastq file
bowtie2 illumina fastq file written 3 months ago by ggman • 40
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0
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178
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Cufflinks produces empty transcript.gtf files
fasta bowtie2 cufflinks rna-seq bam written 3 months ago by william.mcentegart • 0
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1
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210
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1
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Number of reference sequence contigs in sam/bam header does not match the number in my fasta
fasta bowtie2 contig sam bam written 4 months ago by marcusanaymik • 10 • updated 4 months ago by Brian Bushnell ♦ 13k
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156
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mirBase mature microRNA sequences have base U instead of base T. Should I change or not?
mirbase bowtie2 alignment small rna written 4 months ago by bioinforesearchquestions • 80
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182
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Signification of Bowtie2 Metrics file
bowtie2 bowtie rna-seq written 4 months ago by jlncrnt • 0
6
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295
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Bowtie2 throws error no. 139
software error bowtie2 ngs alignment sequencing written 4 months ago by anupriyaverma1408 • 100
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2
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253
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2
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how to keep common reads in paired end reads if the number of reads are not same in read1.fq and read2.fq
perl bowtie2 sed rna-seq awk written 4 months ago by ak93sharma • 10 • updated 4 months ago by shenwei356 • 3.1k
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615
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Bowtie2-build cannot build an index
bowtie2 index written 4 months ago by Gary • 380 • updated 4 months ago by Devon Ryan ♦ 69k
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258
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Different alignments rates with bwa mem (0%) and bowtie2 (82%)
bowtie2 bwa written 5 months ago by James Ashmore • 1.7k
2
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1
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854
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1
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what is the mean of 'Error running 'prep_reads' ???
bowtie2 tophat2 written 22 months ago by F • 2.6k • updated 5 months ago by Biostar ♦♦ 20
5
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1
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268
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1
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I want to know about the actual function of Bowtie?
bowtie2 written 5 months ago by barrypraveen • 0 • updated 5 months ago by Brian Bushnell ♦ 13k
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getting the whole of rRNA.fa for ecoli
ribo-seq bowtie2 written 23 months ago by F • 2.6k • updated 5 months ago by Biostar ♦♦ 20
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