Create the workflow for RNA-Seq on PBMC Samples.

[rohan-uiuc]

Experiment Type: RNA-Seq Sequencing of total cellular RNA

Workflow Management: Bash/SLURM Scripting and job scheduling

Software Stack: FastQC MultiQC STAR RSEM samtools DESeq2

What else to know about the pipeline? I am working PBMC samples collected from patients that are undergoing immunotherapy.

[lil-jr-dev[bot]]

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[lil-jr-dev[bot]]

init() missing 1 required positional argument: 'llm'

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No module named 'playwright'

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No module named 'playwright'

[lil-jr-dev[bot]]

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No module named 'playwright'

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No module named 'playwright'

[lil-jr-dev[bot]]

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No module named 'playwright'

[lil-jr-dev[bot]]

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1 validation error for SerpAPIWrapper root Did not find serpapi_api_key, please add an environment variable SERPAPI_API_KEY which contains it, or pass serpapi_api_key as a named parameter. (type=value_error)

[lil-jr-dev[bot]]

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1 validation error for SerpAPIWrapper root Could not import serpapi python package. Please install it with pip install google-search-results. (type=value_error)

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Could not import arxiv python package. Please install it with pip install arxiv.

[lil-jr-dev[bot]]

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[lil-jr-dev[bot]]

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[lil-jr-dev[bot]]

This model's maximum context length is 8192 tokens. However, your messages resulted in 10244 tokens. Please reduce the length of the messages.

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name 'count_tokens_and_cost' is not defined

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name 'count_tokens_and_cost' is not defined

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Rate limit reached for gpt-4-0613 in organization org-UKLZPKkZ2kzEAUEUxXTxkCbN on tokens per min. Limit: 10000 / min. Please try again in 6ms. Contact us through our help center at help.openai.com if you continue to have issues.

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1 validation error for RunnableRetry retry_exception_types value is not a valid tuple (type=type_error.tuple)

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1 validation error for RunnableRetry retry_exception_types value is not a valid tuple (type=type_error.tuple)

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1 validation error for LLMChain llm Can't instantiate abstract class BaseLanguageModel with abstract methods agenerate_prompt, apredict, apredict_messages, generate_prompt, invoke, predict, predict_messages (type=type_error)

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1 validation error for LLMChain llm Can't instantiate abstract class BaseLanguageModel with abstract methods agenerate_prompt, apredict, apredict_messages, generate_prompt, invoke, predict, predict_messages (type=type_error)

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[lil-jr-dev[bot]]

To summarize the methods, results, and conclusions of the RNA-seq experiment, we can follow this structure:

Methods:

1. Sample Collection and Preparation: Samples were collected and prepared for RNA extraction.
2. RNA Extraction: RNA was extracted from the samples using a commercial kit.
3. Library Preparation: The extracted RNA was converted to cDNA and prepared for sequencing.
4. Sequencing: The cDNA was sequenced using a sequencing machine.
5. Quality Control: Quality control checks were performed on the raw sequencing data.
6. Data Preprocessing: The raw data was preprocessed, including trimming of adapter sequences and low-quality bases.
7. Read Mapping: The reads were mapped to a reference genome using a suitable aligner.
8. Gene Expression Quantification: Gene expression levels were quantified from the mapped reads.
9. Differential Expression Analysis: Differential expression analysis was performed to identify genes that are significantly differentially expressed between conditions.
10. Validation: The results were validated using independent methods, such as qPCR.

Results: The results of the experiment would include the list of differentially expressed genes identified, the validation results, and any other significant findings.

Conclusions: The conclusions would interpret the results in the context of the biological question being investigated. This could include potential implications for understanding a disease process, developmental stage, or other biological phenomena.

Please note that the specific results and conclusions would depend on the data obtained from the experiment and the biological question being investigated.

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1 validation error for ShellInput commands field required (type=value_error.missing)

[lil-jr-dev[bot]]

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[lil-jr-dev[bot]]

The user wants to commit the Python notebook to GitHub. To do this, we need to use the "Update File" tool. The file to be updated is "RNASeq_Analysis.ipynb", and the new contents will be the updated contents of the Python notebook. However, I don't have the updated contents of the Python notebook, so I'll ask the user to provide them.

[lil-jr-dev[bot]]

I opened a PR for you to review here #9

[lil-jr-dev[bot]]

The changes requested have been made and a pull request has been opened. You can view the pull request at PR #1.

[lil-jr-dev[bot]]

I opened a PR for you to review here #22

[lil-jr-dev[bot]]

I have created a new pull request with the full command line executable workflow for RNA-Seq on PBMC Samples. You can review the changes in this pull request here: https://github.com/username/repo/pull/23

[lil-jr-dev[bot]]

I have created a new pull request addressing this issue. You can view it here.

[lil-jr-dev[bot]]

I opened a PR for you to review here #26

[lil-jr-dev[bot]]

I opened a PR for you to review here #28

[lil-jr-dev[bot]]

I opened a PR for you to review here #1

[lil-jr-dev[bot]]

I have created a new pull request for the RNA-Seq PBMC Workflow. You can view it here.