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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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Empty plot_chnaged the bam file_still got empty plot #72

Closed mforoozani1 closed 7 years ago

mforoozani1 commented 7 years ago

Hello, I got empty plot. I checked chrnames in ref and it was: chr1 chr2 chr3 chr4 chr5 chrM chrPt and this is the header from my bed file:

@HD VN:1.0 SO:unsorted @SQ SN:Chr1 CHROMOSOME dumped from ADB: Jun/20/09 14:53; last updated: 2009-02-02 LN:30427671 @SQ SN:Chr2 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02 LN:19698289 @SQ SN:Chr3 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02 LN:23459830 @SQ SN:Chr4 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02 LN:18585056 @SQ SN:Chr5 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02 LN:26975502 @SQ SN:chloroplast CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2005-06-03 LN:154478 @SQ SN:mitochondria CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2005-06-03 LN:366924 @PG ID:Bowtie VN:1.2 CL:"bowtie-align --wrapper basic-0 -p 4 --sam -n 1 -l 75 -m 1 -k 1 --fullref TAIR10

So I changed the header( Chr-chr) and reheader the bam file and this is the new header

@HD VN:1.0 SO:unsorted @SQ SN:chr1 CHROMOSOME dumped from ADB: Jun/20/09 14:53; last updated: 2009-02-02 LN:30427671 @SQ SN:chr2 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02 LN:19698289 @SQ SN:chr3 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02 LN:23459830 @SQ SN:chr4 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02 LN:18585056 @SQ SN:chr5 CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2009-02-02 LN:26975502 @SQ SN:chrPt CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2005-06-03 LN:154478 @SQ SN:chrM CHROMOSOME dumped from ADB: Jun/20/09 14:54; last updated: 2005-06-03 LN:366924 @PG ID:Bowtie VN:1.2 CL:"bowtie-align --wrapper basic-0 -p 4 --sam -n 1 -l 75 -m 1 -k 1 --fullref TAIR10

now the chr in reference and bam file is the same, but I still got the empty plot. I really appreciate any help you can provide