Saesha Verma

13 Questions 4 Answers 0 Followers

Questions related from Saesha Verma

What are the most effective cryopreservation protocols for agarolytic bacteria in terms of maximizing cell viability and recovery rates post thaw?

I have a consortium of agar-degrading microorganisms on the f/2 agar plate, and they have somewhat liquidated the agar. Now I want to know how to collect the bacterial culture from the plate and...

08 January 2025 899 1 View

How to read in multiple files in R and then make a phyloseq object ?

I want to do microbiome analysis using R, for which I have three folders that contain ASV data, metadata i.e. sample data, and taxonomy data for 56 sample studies. I want to read the data in those...

20 May 2024 5,123 2 View

How to create a merged phyloseq object using ASV, taxa, metadata and tree?

I have 10 pre-processed studies for which I have prepared ASV tables, Taxa tables, Metadata, and phylogenetic trees. Now I want to merge these studies and create and single or merged phyloseq...

18 April 2024 7,205 1 View

How to determine whether the .fastq file is single or paired end?

@SRR8393705.1 1...

12 April 2024 6,068 0 View

What should I do as I am encountering issue in running trimmomatic-v-0.39 in windows 11 ?

The issue is related to illumina clip command. Error: Exception in thread "main" java.lang.NumberFormatException: For input string: "/Users/Saesha...

09 March 2024 5,093 2 View

Why I am not able to open ASV table generated after pre-processing 16S rRNA sequences?

When I write this command to generate the ASV table write.csv(seqtab31.nochim, file = "ASV_table31.csv", row.names = FALSE) The file is not able to open "The text file contains more data that...

25 October 2023 5,622 0 View

Is loss of 80% sequences after chimera removal in 16s rRNA preprocessing normal? if not what should I do?

SRR no. input filtered denoisedF denoisedR merged Nonchim % drop SRR15372855 210711 186522 175583 176162 116563 36509 83% SRR15372856 209697 183184 173837 174328 127588 38205 82% SRR15372857...

22 October 2023 9,100 3 View

How to resolve issue of 'cannot open connection' error reading a file named as 'Meta_31.txt' in R?

I'm encountering an issue while trying to read a file named 'Meta_31.txt' in R. Despite confirming the file's existence, verifying the file path, and trying various methods (e.g., read.table,...

04 October 2023 6,270 1 View

How to use cutadapt to remove adapter sequences and perform quality control on fastq files containing ?

I have to pre-process around 10,000 fastqQ files containing 16S rRNA sequences. According to the multiQC reports generated before pre-processing the sequences have good quality reads with Q score...

18 August 2023 2,622 3 View

While downloading the fastq-files using SRAtoolkit I am receiving error message. How to troubleshoot it?

Error message- “An error occurred during processing. A report was generated into the file '/home/poorna/ncbi_error_report.txt'. If the problem persists, you may consider sending the file to...

07 August 2023 1,725 1 View

Each time I open terminal it states that fastq-dump command not found. What should I do?

Every time on reopening the terminal in the Linux system, it states that the fastq-dump command is not found. Then I repeat the entire downloading process again and again.

07 August 2023 3,272 3 View

How to view the fastq files in the Linux system?

I have downloaded fastq files but when I open it black screen appears. Is there any specific software or command for viewing the fastq files? I think it is opening in the text editor in Linux system.

25 July 2023 10,066 2 View

How to download multiple fastq files using fastq-dump in Linux system?

I have many SRA accession numbers and I need to download the fastq files. I am using fastq-dump command to download the fastq files in the Linux system but it works for a single accession number....

21 July 2023 274 3 View