Hello I'm trying to get my sorted bam files to read into golden helixs genome broswer. I'm currently using version 2.1.0. Alot of my data comes into the broswer as Did not successfully write coverage data amoung other issues.
I've done this process
1.Download Data from NCBI in form of Fastq/Fasta format
2.Download data from igenome
3.Unzip Igenome data in linux
4.Build alignment Bowtie2-align -x “name of Built index” “.fastq” -S “.Sam”
5. Convert Sam file to Bam file with samtools view -Sb “Sam File” > “Bam File”
6. samtools sort -n*if not sorted for cufflinks “bam file”
The data will go through things like cufflinks/tophats. They are also 7gig files but doesnt work in the broswer.
What can I do to fix this?
I've done this process
1.Download Data from NCBI in form of Fastq/Fasta format
2.Download data from igenome
3.Unzip Igenome data in linux
4.Build alignment Bowtie2-align -x “name of Built index” “.fastq” -S “.Sam”
5. Convert Sam file to Bam file with samtools view -Sb “Sam File” > “Bam File”
6. samtools sort -n*if not sorted for cufflinks “bam file”
The data will go through things like cufflinks/tophats. They are also 7gig files but doesnt work in the broswer.
What can I do to fix this?
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