Previously we looked at proteins and genes identified to be correlated to Covid-19 severity from this...

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Previously we looked at proteins and genes identified to be correlated to Covid-19 severity from this study. The Raw fastq data is deposited at GEO: GSE 157103(See if you can identify the BioProject project ID from the GEO page). In this assignment we will download a few RNA-seq samples from the study and take a look at basic statistics. First, we will obtain the sequencing run information with: esearch -db sra -query PRJNA660067 | efetch -format runinfo > runinfo.csv Obtain the SRR run ID's with (take the first 9 for example): cut -d","f 1 runinfo.csv | head 1. Report at least 5 SRR run IDs for the fastq samples of this study. 2. Report the sex of these 5 samples based on the metadata provided here: SraRun Table.txt If you use my server, the file can also be found here: /data/bio2023/Assignments/Lec09/SraRunTable.txt You can use the command below to get the sex information from the 40th column (Please the command below to help, but you need to revise it to answer the questions). cut -d","f1,40 SraRunTable.txt Second, we will download the fastq files for one of those samples with the command. fastq-dump -X 1000 --split-files SRR12544599 Look at the statistics and output of this sequencing run with the command 3. Is this a paired ended library? Third, run seqkit stats SRR12544599_1.fastq Please note: (i) If you use your own environment or the environment in the classroom or the biou20 image I provided, you need to run conda install -c bioconda seqkit to install the package first. (ii) If you are using the environment provided by me in my server, you do not need to install it. (iii) Some of you use my server but created your own environment; in this case, you still need to install the packages by yourself. 4. How many reads are in this sample? 5. What are the read lengths of this library? Previously we looked at proteins and genes identified to be correlated to Covid-19 severity from this study. The Raw fastq data is deposited at GEO: GSE 157103(See if you can identify the BioProject project ID from the GEO page). In this assignment we will download a few RNA-seq samples from the study and take a look at basic statistics. First, we will obtain the sequencing run information with: esearch -db sra -query PRJNA660067 | efetch -format runinfo > runinfo.csv Obtain the SRR run ID's with (take the first 9 for example): cut -d","f 1 runinfo.csv | head 1. Report at least 5 SRR run IDs for the fastq samples of this study. 2. Report the sex of these 5 samples based on the metadata provided here: SraRun Table.txt If you use my server, the file can also be found here: /data/bio2023/Assignments/Lec09/SraRunTable.txt You can use the command below to get the sex information from the 40th column (Please the command below to help, but you need to revise it to answer the questions). cut -d","f1,40 SraRunTable.txt Second, we will download the fastq files for one of those samples with the command. fastq-dump -X 1000 --split-files SRR12544599 Look at the statistics and output of this sequencing run with the command 3. Is this a paired ended library? Third, run seqkit stats SRR12544599_1.fastq Please note: (i) If you use your own environment or the environment in the classroom or the biou20 image I provided, you need to run conda install -c bioconda seqkit to install the package first. (ii) If you are using the environment provided by me in my server, you do not need to install it. (iii) Some of you use my server but created your own environment; in this case, you still need to install the packages by yourself. 4. How many reads are in this sample? 5. What are the read lengths of this library?

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For questions 4 and 5 you mentioned the need to analyze RNAseq data and obtain read information and ... View the full answer