Merge pull request #16 from NIGMS/fix_broken_links

Fix broken links

tutorial_1-bismark.ipynb

@@ -59,7 +59,7 @@
     "! ~/miniconda3/bin/conda init bash\n",
     "! ~/miniconda3/bin/conda init zsh\n",
     "```   \n",
-    "It would take less time to install some of the tools in this tutorial if you create a new conda environment. But it is a little bit tricky to use a different conda environment within Jupyter in GCP. You can find instructions of how to create a new conda environment [here](https://github.com/STRIDES/NIHCloudLabGCP/docs/How_to_use_conda_envs_as_kernels.ipynb).\n",
+    "It would take less time to install some of the tools in this tutorial if you create a new conda environment. But it is a little bit tricky to use a different conda environment within Jupyter in GCP. You can find instructions of how to create a new conda environment [here](https://github.com/STRIDES/NIHCloudLabGCP/blob/main/docs/create_conda_env.md).\n",
     "</div>"
    ]
   },
@@ -364,7 +364,7 @@
     "\n",
     "All four DNA strands that arise through bisulfite treatment and subsequent PCR amplification can be sequenced with the same frequency in non-directional libraries, while for directional libraries, adapters are attached to the DNA fragments such that only the original top or bottom strands will be sequenced. In the Bismark alignment step, `--directional` is set to default, so only report OT and OB strands.\n",
     "\n",
-    "**Output alignment**. The output .bam files are the binary version of the SAM (Sequence Alignment/Map) format. Please see [here](https://github.com/FelixKrueger/Bismark/tree/master/Docs#bismark-bamsam-output-default) for more detailed explanation of the output .bam/.sam format, where the `XM-tag` is the methylation call string to indicate the methylated status of each C(tyosine) in different contexts: CG (or CpG), CHG or CHH (where H correspond to A, T or C). The methylation call string contains a dot ‘.’ for every position in the BS-read not involving a cytosine,\n",
+    "**Output alignment**. The output .bam files are the binary version of the SAM (Sequence Alignment/Map) format. Please see [here](https://github.com/FelixKrueger/Bismark/blob/master/docs/bismark/alignment.md#bismark-bamsam-output-default) for more detailed explanation of the output .bam/.sam format, where the `XM-tag` is the methylation call string to indicate the methylated status of each C(tyosine) in different contexts: CG (or CpG), CHG or CHH (where H correspond to A, T or C). The methylation call string contains a dot ‘.’ for every position in the BS-read not involving a cytosine,\n",
     "or contains one of the following letters (z,Z,x,X,h,H) for the three different cytosine methylation contexts (UPPER CASE = METHYLATED, lower case = unmethylated).\n",
     "> <img src=\"images/1_bismark_bam.png\" width=\"600\" />\n",
     "\n",
@@ -818,7 +818,11 @@
    ]
   }
  ],
- "metadata": {},
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
  "nbformat": 4,
  "nbformat_minor": 5
 }