bioinfo17

Error with bam files that has paired end reads + singletons

13

Hi, I used merged genome + transcriptome file with Hisat2 to retrieve all reads in my samples, and then converted the bam files to R1. fastq, R2.fastq + singletons files....

Hisat2, stringtie protocol for paired-end and single reads

2

Hi, As per the published hisat2/stringtie protocol, hisat2 is used with paired-end reads. I was wondering if hisat2 can be run using paired-end and singleton/single-read files together using -1, -2...

Hi, I get this error while executing po2group_stats.pl: Bareword found where operator expected at ./po2group_stats.pl line 669, near "s/\.\w+$//r" syntax error at ./po2group_stats.pl line 669, near "s/\.\w+$//r" BEGIN not safe...

error with length percentage cutoff using 0.7 and higher

1

Hello, The taxonomy_assignment_BLAST_V2.py script works great for taxonomic assignment using default parameters. However when I use it with the filtering option "length_percentage" with values equal to or > than 0.7...

assembling nanopore sequenced bacterial transcriptomes

1

Hi, not an issue but will this tool work with bacterial transcriptome? I read through the manual and couldn't find an answer. Since bacterial species don't have introns will this...