How to generate .seq files

[ndfriedman]

Hi there, I am very interested in running bicseq but am struggling to parse the documentation to successfully complete the first step (generating .seq files). I have tried using the modified samtools and sh scripts within the docker container, neither of which worked. Could you please direct me to the explicit steps I should use to complete the first step and generate .seq files? I am having a hard time figuring out which branch on github is functional for my purposes. Thanks so much!

[taoziyu97]

Hi there, I am very interested in running bicseq but am struggling to parse the documentation to successfully complete the first step (generating .seq files). I have tried using the modified samtools and sh scripts within the docker container, neither of which worked. Could you please direct me to the explicit steps I should use to complete the first step and generate .seq files? I am having a hard time figuring out which branch on github is functional for my purposes. Thanks so much!

Hi, I have the same question here recently. Here is my solution.

The key is you should cd path_to_output.

cd /home/out
/home/tools/samtools-0.1.7a_getUnique-0.1.3/samtools view -U BWA,output,N,N /home/data/my.bam

Then you can generate .seq file.

The detailes are in https://www.math.pku.edu.cn/teachers/xirb/downloads/software/BICseq2/FAQ-BICseq2.pdf.