search

virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
Other
131 stars 42 forks source link

No output for the bed file after running amplified_intervals.py #68

Open junchend opened 4 years ago

junchend commented 4 years ago

Dear Viraj,,

I am trying to run AA for my data focus on cancer samples. However, when I runned amplified_intervals.py, no output was there in the bed file, my code is:

/public/software/aaconda2/bin/python2 /public/AmpliconArchitect/src/amplified_intervals.py --bed S1/output/alts.dat --out S1 --bam S1-sort.bam

some lines will be seen in the running process:

0 1001 133 0.0 0 1001 161 0.0 0 1001 174 0.0 0 1001 64 0.0 0 1001 67 0.0 0 1001 51 0.0

but the bed file is 0 size.

Should I downsample the bam file first?

Thank so much!

Juncheng

alhafidzhamdan commented 4 years ago

In my case, each time i got a bed file of size 0, looking at the actual CN file there was no contigs with CN>5 (default cut off).