I have received two paired end fastq files to analyze and when I look at the header I realized the following:
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Strange Illumina fastq header
Hi all,
I have received two paired end fastq files to analyze and when I look at the header I realized the following:
...Last edited by chariko; 07-27-2016, 03:56 AM. -
Trinity output
Hi,
Trinity outputs to my understanding components and isoforms, or I think now they call them genes and transcripts, so can someone explain to...Last edited by illinu; 11-13-2014, 05:57 AM. -
samtools sam to bam header
Hi
I am trying to sort my bam file using samtools 0.1.19-44428cd
with the following command:
samtools sort test_sequence.bam...Last edited by mattbawn; 05-28-2014, 10:51 AM. -
Issue with BGZF and Samtools
Hi,
I'm a college student working on a parallel version of Samtools project.
I have to use BGZF to compress blocks of data in order... -
BWA gives no alignment lines in SAM file
Good morning,
I am trying to map simulated reads generated from GemSIM to an index generated from a multi-fasta of the CLJU (bacteria)... -
"samtools: no @sq lines in the header" - metagenome!
Hi,
I'm trying to clean a bam file, by deleting reads that failed QC (for instance), and writing a new bam file. When I run the following... -
Cufflinks bam header size too large
When running cufflinks on my accepted_hits.bam files from tophat, I get this output, truncated as there are many CIGAR errors.
...Code:You are
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What is the header format for Interval List in PicardTools?
Hi,
I have aligned paired-end read data from from a gene resequencing project, and am attempting to run the CalculateHsMetrics tool from... -
insert PG and CL tags into BAM header with BWA
What do you recommend I use to insert full command line into the BAM header created with BWA. BWA already creates this:
@PG ID:bwa PN:bwa... -
samtools view error after reheader
I am currently having an issue with samtools view for conversion of .sam to .bam. After replacing the header of my .sam in order to match the ref contigs... -
how to convert sam to bam with EOF marker in header
I aligned short reads by an nonpublished aligner. Then I converted the
alignments to sam, then bam, and sote bam. It looks they worked for
... -
help me on reheader ".bam for indexing and mpileup
I aligned short reads by an nonpublished aligner. Then I converted the alignments to sam, then bam, and sote bam. They worked for me. Now, I intend to... -
Parsing error in BAM header
Hi~ I am pretty new to this area, having a hard time with these huge files..
I wanted to use IndelGenotyperV2 (from GATK) with my newly...
