hbctraining / intro-to-rnaseq-hpc-o2 Goto Github PK

Change unix_workshop to unix_lesson in all lessons.

consider splitting it or in the way in which we teach it

Link to IGV tutorial for now until we create the module materials for IGV and publication quality figures and we can link to that

keep a line or two describing and introducing it, link the old materials here as additional material

Move the automation to after salmon.

Automate salmon run instead of STAR as the focus, and remove featurecounts. Add qualimap and multiqc.

Hi, thanks for the concise overview of a sam file but I am struggling with some of the descriptors. Like the one for SEQ, in the spec on www.htslib.org/doc/sam.html described as

10 | SEQ | query SEQuence on the same strand as the reference

which could be ambiguous when it is not known what strand of the reference has been used (upper, lower, both?) for the aligning.

In the intro on this site SEQ is described to be "the raw sequence" as found in the fastq file:

Finally, you have the data from the original FASTQ file stored for each read. That is the raw sequence (SEQ) ...

But does the SEQ not give the sequence present in the fasta file used as the reference for aligning, which is normally the sense strand? Not the raw sequence. This difference is important when the mapped raw read has been on the reverse (antisense) strand, which is annotated in the flag with 16.

Thus, for mapped reads antisense to the reference would one not expect the reverse compliment sequence as SEQ (and thus not the raw fastq sequence)?

use this as a template and update the link to lessons - https://github.com/hbctraining/Intro-to-ChIPseq/blob/master/README.md

It is okay if there is not an actual schedule, as long as each lesson has a time associated with it.