pacbio db and las files
Dear all,
I would like to use this software to look at the quality of my pacbio reads: https://dazzlerblog.wordpress.com/2015/11/06/intrinsic-quality-values/
However, it requires db and las files. I only have .bam and .fastq files. Does anybody know what these files are and how I can get them?
Thanks.
C.
db
pacbio
las
next-gen
• 1,627 views
•
link
updated
by
Ram
•
written
by
biomagician
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Error with hera not finding the index
written by biomagicianDear all, I have created a Hera index using: ./output/software/hera/build/hera_build --fasta output/genome/celegans/ref/seq/celegans.fa --gtf output/genome/celegans/ref/annotation/celegans.gtf --outdir output/genome/celegans/ref/index/hera/ This creates 3 files: index, reference.inf, transcripts.fasta I then …
-
Can I open a BAM file without a header in Rsamtools?
written by biomagicianDear all, I am trying to analyse the quality of reads from a BAM file but the BAM file does not have a header so …
-
dextract multi-threadding possible?
written by biomagicianDear all, Does anybody know if the dextract command can use more than one core and how? https://dazzlerblog.wordpress.com/command-guides/dextractor-command-guide/ Best wishes, C.
-
fasta2DB command from DAZZ_DB
written by biomagicianDear all, I am trying to make a database from a fasta file that comes from pacbio sequencing using: fasta2DB -f output/reads/pacbio/sx.fa https://dazzlerblog.wordpress.com/command-guides/dazz_db-command-guide/#fasta2DB but I …
-
How to install DASQV?
written by biomagicianDear all, I would like to use the DASQV software to scrub pacbio reads. https://github.com/thegenemyers/DASCRUBBER Does anybody know how to install it? Thanks. C.
-
Using the align() function of the Rsubread package; error: unrecognized option `--gtfFeature'
written by biomagicianDear all, I am using the bioconductor package Rsubread to align reads to a genome: Rsubread::align(index="output/genome/ref/index/subread/celegans", readfile1='output/reads/trimmed/pooled/altadena1.fastq.gz', input_format="gzFASTQ",output_format="BAM", output_file='output/out2.bam',unique=TRUE,indels=5, nthreads = 8, useAnnotation = TRUE, …
-
Can STAR work with compressed .gz FASTQ input?
written by biomagicianDear all, I would like to align some reads to a reference using STAR. The following command works perfectly: STAR --genomeDir output/spiking/index/star --readFilesIn reads.fastq --outFileNamePrefix …
-
Tophat 'prep_reads error": beginning of quality values record not found!
written by mmitra •Hi all, I ran tophat on my fastq file and I got the following error: [2015-09-02 11:23:58] Beginning TopHat run (v2.1.0) ----------------------------------------------- [2015-09-02 11:23:58] Checking …
-
standalone blast , database error
written by tcf.hcdgHello I would like to blast my sequences using NCBI standalone blast. I downloaded the lates version of blast(2.2.31+). After downloading I extract the files …
-
Tophat failed at 'Mapping left_kept_reads to transcriptome'
written by biocybermanI am trying to run tophat for color-space data. The error is not very helpful for me to know what's wrong. Any help is much …
DAMAPPERis the program that is producing those files (https://dazzlerblog.wordpress.com/command-guides/damapper-commands/ ).