HughCruiseJr

Thank you so much for your reply, my repeat file is from UCSC specifically for HG38, cause when I did the annotations I used GTF file for HG38? also the...

I ran the suggestions that you gave earlier, "a7@bios-76-1:~/Output/SPRINT$ python2 sprint_from_bam.py --rp $HOME/Output/Human/SRR2040582.regular.txt $HOME/Output/STAR_Output/Aligned_B1_53632Aligned.sortedByCoord.out_.bam $HOME/Output/GRCh38.primary_assembly.genome.fa $HOME/Output/Sprint_B1_53632 /usr/bin/samtools" but still its exiting. I am little overwhelmed.  Thank you again in...

Thank you doer your response, my program ran, but all the resulting files were 0KB, only aligned SAM and genome_all_zz.dedup are having data. I got the BAM files from STAR...

Thank you for your reply feng. Can you please let me know any other way to download the files instead of Pan.Baidu, cause it is taking forever to download the...

Thank you for your reply, I was able to retrieve files, and I have them all in same directory to avoid confusion. This is the code that I am writing...

Thank you so much Feng! I was able to prepare, and then I ran main function but after running for 10-12 minutes its stopping, seems like not able to find...

Dear Feng, Thank you for your response, samtools and BWA are already downloaded with correct version on my system, still facing the same problem as mentioned above. This is the...

Thank you Feng! truly appreciate your help. Even updating the SAMTOOLS to what is required version, we were able to see the error, getting SAMTOOLS help menu because in file...

Thank you Feng for your reply, I am using the exact same version as required for samtools.  Still I am getting the same output error, it is not able...

Hey Feng, I tried resetting everything, but the problem persist, since starting I am using your binaries. I am getting the same errors, all.sam file is not created in genome....