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Hi. Thanks for the feedback. Do you mean the 2 qc parameter? Total umi and total genes in the violin plot? Yes they can't be compared directly via violin plot since y axis is different for both. The correlation plot is helpful to see how much correlation you see. Usually correlation is high. I hope I understood your point of view.

Yes cell ranger pipeline starts from fastq to count. U can refer the 2nd part of this video to know more.

​@@bioinfquestsI am reaching out to inquire about Cell Ranger and its compatibility with our in-house sequencing setup. We currently have our own sequencer and would like to explore the possibility of using Cell Ranger to generate counts from our own BCL data. As I have limited hands-on exposure in library preparation, I wanted to understand if any modifications or changes are required in the library preparation process to use Cell Ranger effectively. Could you please provide some insights into how Cell Ranger works and whether it can be seamlessly integrated with our existing library preparation workflow?

Glad it was helpful!

Thanks for encouraging feedback. Appreciate if you shout out about my channel in your network. This will boost my channel. I will soon be posting some videos on seurat.

If I am not wrong it's www.nature.com/articles/s41596-018-0073-y Is this video useful? Any positive or negative feedback would be valuable.

@@bioinfquests Yes, this video is very useful! I keep coming back to it. :D THANK YOU!!

Thanks for your encouraging feedback. Please share about my channel in your network. This will boost my channel. Yes I will soon be posting some videos on seurat.

Most of these tools can be installed on macos also. So u can run on macos.

bp basepairs

For text size, u can use element_text function and set size parameter. for font type, use family parameter.

For context I’m a computer scientist who is doing research into computation biology. I have almost no biology background so videos like this make my life so much easier when reading papers

Thanks. Fastq file link is provided in the description. The fastqtofasta is provided by shasta. it will be there in the shasta installation directory. you need to use full path to the script or copy the script in the data folder and run from there

Thanks sir for the reply and valuable suggestions. I will try.

Sir..can you provide any classes or traning on the hands on linux bioinformatics? Pls provide your contact No.

Its the count of each category which is specified on x axis. it will be automatically counted. When we specify x with a column, R will xount frequency of each category and consider that as y. Hope it answers.

Better to save the data of excel in tab separate value or comma separated csv file and use same read.table or read.csv method to load the data in df and plot. Although there are package like gdata or xlxs are there which can be used to read excel data.

See there are 2 possibilities 1. You have reference genome already known e.g. human. 2. You do not have reference genome e.g. a new species is identified and you plan to sequence them. In former case you can use already known genome reference information to guide the assembly process. In second case, you are newly doing assembly to generate reference genome. In first case at least you can compare the assembly with reference to infer how close your sample is with the reference one while in second case you have to trust or validate the assembly based on assembly statistics or some other literature evidence or prior experimental evidence.

Yes am planning to add few videos. Thanks for the suggestions.

How many categories u are getting. If i understood correctly u r saying that you have so many categories, each bar overlap with nearby bar? Can you elaborate more since its not clear. If you are saying that y axis value is high, you can represent frequency as percentage as well.

@@bioinfquests i have about 6 categories, when i do bar plot, the results are the count of each category. the length of the database is 250,000 rows. when I do count for these categories the frequency i.e. number get mixed up

Sorry not able to understand what number gets mixed up means..since there are 6 categories and total 250k values, u will get 6 frequency values which will add to total 250k. So it should plot fine, x being the category and y being the value.

@@bioinfquests hi thank you for this. I have about 6 categories i.e. bars and the dataset is very long 250,000 records. so when I have some of them use numbers in the 100,000 the get mixed up. wonder if i make adjustments to make numbers display well without getting inter linked. I actually thought of making the division in the dataset now by 1000 for example

@@ahmed007Jaber you can display the frequency as percentage as well so that y axis will be in the scale of 0-100.

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Thanks for the suggestion. Will keep this in mind and create a session on this.

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