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Preview error #11

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920f383
testing preview error
RossCampbellNIH2 Dec 19, 2023
d4b357c
trying to find preview error
RossCampbellNIH2 Dec 19, 2023
981f8d5
trying to find preview error
RossCampbellNIH2 Dec 19, 2023
df1543f
trying to find preview error
RossCampbellNIH2 Dec 19, 2023
d5a096b
trying to find preview error
RossCampbellNIH2 Dec 19, 2023
b1a277a
fix preview issue
RossCampbellNIH2 Dec 19, 2023
6054491
Delete test.ipynb
rosscampbellNIH Dec 19, 2023
37c9f87
Fix bowtie2 path
rosscampbellNIH Dec 20, 2023
b88f9ed
remove ! from python block
RossCampbellNIH2 Dec 20, 2023
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79 changes: 39 additions & 40 deletions ATACseq_BonusTutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -147,10 +147,10 @@
" \n",
" Make sure you include the `!` in front of your command! \n",
" \n",
" ``` \n",
"gsutil -m cp $original_bucket/InputFiles/Liver* Tutorial1/InputFiles/\n",
"gsutil -m cp $original_bucket/InputFiles/Muscle* Tutorial1/InputFiles/\n",
" ```\n",
" \n",
"`gsutil -m cp $original_bucket/InputFiles/Liver* Tutorial1/InputFiles/` \n",
"`gsutil -m cp $original_bucket/InputFiles/Muscle* Tutorial1/InputFiles/`\n",
" \n",
"\n",
"</details>\n"
]
Expand Down Expand Up @@ -181,9 +181,8 @@
"<details>\n",
" <summary>Click for help</summary>\n",
" \n",
" ``` \n",
"gsutil -m cp $original_bucket/RefGenome/* Tutorial1/RefGenome\n",
" ```\n",
" \n",
"`gsutil -m cp $original_bucket/RefGenome/* Tutorial1/RefGenome`\n",
"\n",
"</details>\n"
]
Expand Down Expand Up @@ -235,9 +234,9 @@
"<details>\n",
" <summary>Click for help</summary>\n",
" \n",
" ``` \n",
" fastqc -t $numthreadsint -q -o Tutorial1/QC Tutorial1/InputFiles/*fastq.gz\n",
" ```\n",
"\n",
" `fastqc -t $numthreadsint -q -o Tutorial1/QC Tutorial1/InputFiles/*fastq.gz`\n",
"\n",
"\n",
"</details>\n"
]
Expand Down Expand Up @@ -268,9 +267,9 @@
"<details>\n",
" <summary>Click for help</summary>\n",
" \n",
" ``` \n",
" multiqc -o Tutorial1/QC -f Tutorial1/QC 2> Tutorial1/QC/multiqc_log.txt\n",
" ```\n",
"\n",
" `multiqc -o Tutorial1/QC -f Tutorial1/QC 2> Tutorial1/QC/multiqc_log.txt`\n",
"\n",
"</details>\n"
]
},
Expand All @@ -289,7 +288,7 @@
"metadata": {},
"outputs": [],
"source": [
"! <YOUR COMMAND HERE>"
"<YOUR COMMAND HERE>"
]
},
{
Expand All @@ -300,10 +299,10 @@
"<details>\n",
" <summary>Click for help</summary>\n",
" \n",
" ``` \n",
" dframe = pd.read_csv(\"Tutorial1/QC/multiqc_data/multiqc_fastqc.txt\", sep='\\t')\n",
" display(dframe)\n",
" ```\n",
" This is a python command, so we don't use a `!` at the start. \n",
" `dframe = pd.read_csv(\"Tutorial1/QC/multiqc_data/multiqc_fastqc.txt\", sep='\\t')` \n",
" `display(dframe)`\n",
"\n",
"</details>\n"
]
},
Expand Down Expand Up @@ -333,9 +332,9 @@
"<details>\n",
" <summary>Click for help</summary>\n",
" \n",
" ``` \n",
" trimmomatic PE -threads $numthreadsint Tutorial1/InputFiles/Liver_sub_1.fastq.gz Tutorial1/InputFiles/Liver_sub_2.fastq.gz Tutorial1/Trimmed/Liver_trimmed_R1.fastq.gz Tutorial1/Trimmed/Liver_unpaired_R1.fastq.gz Tutorial1/Trimmed/Liver_trimmed_R2.fastq.gz Tutorial1/Trimmed/Liver_unpaired_R2.fastq.gz ILLUMINACLIP:Tutorial1/RefGenome/NexteraPE.fa:2:30:10 LEADING:3 TRAILING:3\n",
" ```\n",
"\n",
"`trimmomatic PE -threads $numthreadsint Tutorial1/InputFiles/Liver_sub_1.fastq.gz Tutorial1/InputFiles/Liver_sub_2.fastq.gz Tutorial1/Trimmed/Liver_trimmed_R1.fastq.gz Tutorial1/Trimmed/Liver_unpaired_R1.fastq.gz Tutorial1/Trimmed/Liver_trimmed_R2.fastq.gz Tutorial1/Trimmed/Liver_unpaired_R2.fastq.gz ILLUMINACLIP:Tutorial1/RefGenome/NexteraPE.fa:2:30:10 LEADING:3 TRAILING:3`\n",
"\n",
"</details>\n"
]
},
Expand All @@ -357,9 +356,9 @@
"<details>\n",
" <summary>Click for help</summary>\n",
" \n",
" ``` \n",
" trimmomatic PE -threads $numthreadsint Tutorial1/InputFiles/Muscle_sub_1.fastq.gz Tutorial1/InputFiles/Muscle_sub_2.fastq.gz Tutorial1/Trimmed/Muscle_trimmed_R1.fastq.gz Tutorial1/Trimmed/Muscle_unpaired_R1.fastq.gz Tutorial1/Trimmed/Muscle_trimmed_R2.fastq.gz Tutorial1/Trimmed/Muscle_unpaired_R2.fastq.gz ILLUMINACLIP:Tutorial1/RefGenome/NexteraPE.fa:2:30:10 LEADING:3 TRAILING:3\n",
" ```\n",
" \n",
"`trimmomatic PE -threads $numthreadsint Tutorial1/InputFiles/Muscle_sub_1.fastq.gz Tutorial1/InputFiles/Muscle_sub_2.fastq.gz Tutorial1/Trimmed/Muscle_trimmed_R1.fastq.gz Tutorial1/Trimmed/Muscle_unpaired_R1.fastq.gz Tutorial1/Trimmed/Muscle_trimmed_R2.fastq.gz Tutorial1/Trimmed/Muscle_unpaired_R2.fastq.gz ILLUMINACLIP:Tutorial1/RefGenome/NexteraPE.fa:2:30:10 LEADING:3 TRAILING:3`\n",
"\n",
"</details>\n"
]
},
Expand Down Expand Up @@ -391,12 +390,12 @@
"<details>\n",
" <summary>Click for help</summary>\n",
" \n",
" ``` \n",
" fastqc -t $numthreadsint -q -o Tutorial1/Trimmed Tutorial1/Trimmed/*fastq.gz\n",
" multiqc -o Tutorial1/QC -f Tutorial1/Trimmed 2> Tutorial1/QC/multiqc_log.txt\n",
" dframe = pd.read_csv(\"Tutorial1/QC/multiqc_data/multiqc_general_stats.txt\", sep='\\t')\n",
" display(dframe)\n",
" ```\n",
" \n",
" `fastqc -t $numthreadsint -q -o Tutorial1/Trimmed Tutorial1/Trimmed/*fastq.gz` \n",
" `multiqc -o Tutorial1/QC -f Tutorial1/Trimmed 2> Tutorial1/QC/multiqc_log.txt` \n",
" `dframe = pd.read_csv(\"Tutorial1/QC/multiqc_data/multiqc_general_stats.txt\", sep='\\t')` \n",
" `display(dframe)` \n",
" \n",
"</details>"
]
},
Expand Down Expand Up @@ -456,9 +455,9 @@
"<details>\n",
" <summary>Click for help</summary>\n",
" \n",
" ``` \n",
" bowtie2 -p $numthreadsint -x Tutorial1/RefGenome/GRCz11 -1 Tutorial1/Trimmed/Liver_trimmed_R1.fastq.gz -2 \n",
" ```\n",
"\n",
" `bowtie2 -p $numthreadsint -x Tutorial1/RefGenome/GRCz11 -1 Tutorial1/Trimmed/Liver_trimmed_R1.fastq.gz -2 Tutorial1/Trimmed/Liver_trimmed_R2.fastq.gz -S Tutorial1/Mapped/Liver.sam`\n",
"\n",
"</details>\n"
]
},
Expand Down Expand Up @@ -506,10 +505,10 @@
"<details>\n",
" <summary>Click for help</summary>\n",
" \n",
" ``` \n",
" samtools view -q 10 -bhS Tutorial1/Mapped/Liver.sam | samtools sort -o Tutorial1/Mapped/Liver.bam -\n",
" print(\"done\")\n",
" ```\n",
"\n",
" `samtools view -q 10 -bhS Tutorial1/Mapped/Liver.sam | samtools sort -o Tutorial1/Mapped/Liver.bam -` \n",
" `print(\"done\")`\n",
"\n",
"</details>\n"
]
},
Expand Down Expand Up @@ -618,12 +617,12 @@
"metadata": {
"environment": {
"kernel": "python3",
"name": "common-cpu.m113",
"name": "common-cpu.m114",
"type": "gcloud",
"uri": "gcr.io/deeplearning-platform-release/base-cpu:m113"
"uri": "gcr.io/deeplearning-platform-release/base-cpu:m114"
},
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (Local)",
"language": "python",
"name": "python3"
},
Expand Down