Tag: bowtie2-align

(ERR): bowtie2-align exited with value 13

bowtie2 – (ERR): bowtie2-align exited with value 13 1 I am trying to run bowtie2. but following error are occuring everytime bowtie2 –very-fast-local -x bowtie -q -1 R1.fastq -2 R2.fastq -s aligned.sam Saw ASCII character 10 but expected 33-based Phred qual. terminate called after throwing an instance of ‘int’ Aborted…

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Use RSEM and Bowtie2 to align paired-end sequences

Use RSEM and Bowtie2 to align paired-end sequences 0 I want to use rsem-calculate-expression and bowtie2 aligner to align paired-end sequence based on the following conditions: 2 processors generate BAM file very fast bowtie2 sensitivity append gene/transcript name My code: rsem-refseq-extract-primary-assembly GCF_000001405.31_GRCh38.p5_genomic.fna GCF_000001405.31_GRCh38.p5_genomic.primary_assembly.fna rsem-prepare-reference –gff3 GCF_000001405.31_GRCh38.p5_genomic.gff –bowtie2 –bowtie2-path /bowtie2-2.4.5-py39hd2f7db1_2 –trusted-sources…

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error while loading shared libraries

Question: Question: bowtie2-align-s: error while loading shared libraries Abhinav26 days ago Question: bowtie2-align-s: error while loading shared libraries /home/emilyw/.conda/envs/shotgun_134/bin/bowtie2-align-s: error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory (ERR): Description of arguments failed! Exiting…

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Issue with fastq after converting phred 64 to phred 33 quality scores

Hello, I ran seqtk seq -VQ64 read1.fastq.gz > read1_phred33.fastq to convert my 64 based phred score reads to 33 based phred score phred reads. However when I attempted to run them through tophat alignment I got this error: Saw ASCII character 4 but expected 33-based Phred qual. terminate called after…

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Weird error from BWA and BOWTIE2

Weird error from BWA and BOWTIE2 1 Hi community, Recently I have used BWA and Bowtie2 to align simulated DNA sequencing data to test our sequencing simulator. I got some errors from both aligners: BWA: submit.sh: line 48: 6881 Segmentation fault (core dumped) BOWTIE2: terminate called after throwing an instance…

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bowtie2-align died with signal 24 (XCPU) (core dumped)

(ERR): bowtie2-align died with signal 24 (XCPU) (core dumped) 0 Hi all, it is my first time using bowtie2, and I have a problem. I conducted the following command for reads mapping: bowtie2 -q –local -x mm10 -U SRR5839956_trimmed.fq -S SRR5839956.sam It created a 600MB sam file then come with…

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