Kathleen Chappell (Keating)

I ran through the lesson and all exercises and was able to follow the instructions/exercises as expected. I did not see any difference with respect to available functions/options (or the...

Hi Aaron, This is my BAM header. Do you think there will be an issue with the pipes? ``` $ samtools view -H pass.fastq.bwa.sorted.bam @HD VN:1.3 SO:coordinate @SQ SN:gi|215104|gb|J02459.1|LAMCG LN:48502...

If I run the command you suggested, I get the read names: ``` $ samtools view pass.fastq.bwa.sorted.bam | cut -f 1 | sort | uniq -c 1 ch128_file14 1 ch128_file15...

Can you give an example of what your input sequence names look like, as well as what portion of the name the splitting command keeps? I want to make sure...

I wanted to follow up again on which field I should be keeping when I modify the script. In the example of "ch128_file14", do I need "ch128" or "file14"? Thanks,...