fix some links

labs/lab_6 2024.md

@@ -132,7 +132,7 @@ because it was simulated using chr_1 as a reference, but for real data this will
 2. The bitwise flag. This number tells us about the read and its mapping. There are multiple different possible 
 things the read could have, and the total value of the number can the translated into that information. For example, 
 if the read is paired, add + 1. If the read is unmapped, add + 8. Therefore, if the final number is 9, that means it
-is paired and unmapped. The decoding of all possible numbers can be found (here)[https://broadinstitute.github.io/picard/explain-flags.html].
+is paired and unmapped. The decoding of all possible numbers can be found [here](https://broadinstitute.github.io/picard/explain-flags.html).
 3. The contig that the read is mapped to
 4. The starting location where the read maps to, on the contig.
 5. The mapping quality. 60 is the highest (generally) and means high confidence in where the read is mapped.
@@ -146,7 +146,7 @@ The lowest value is 0, which means it is equally likely to map elsewhere.
 12. Any extra flags.
 
 ## Questions
-1. For one read, you find a CIGAR string "12M1I113M". Refer to the (sam format manual)[https://samtools.github.io/hts-specs/SAMv1.pdf] and figure out
+1. For one read, you find a CIGAR string "12M1I113M". Refer to the [sam format manual](https://samtools.github.io/hts-specs/SAMv1.pdf) and figure out
 what this means for how the read is aligned.
 2. Find the read with the lowest mapping quality in your dataset using command line programs.
 3. How are the reads ordered in this sam file?