User: jayeshkumarsundaram

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Posts by jayeshkumarsundaram

<prev • 13 results • page 1 of 2 • next >
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Comment: A: Kallisto: Estimated average fragment length
... Attached more information .... Command: kallisto quant -t 4 -i kallisto_index -o ./ SRR6250323_1.fastq.gz SRR6250323_2.fastq.gz SRR6250324_1.fastq.gz SRR6250324_2.fastq.gz Output: [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [inde ...
written 15 days ago by jayeshkumarsundaram0 • updated 15 days ago by GenoMax96k
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Kallisto: Estimated average fragment length
... I used kallisto tool for RNA-seq quantification of pair-end reads. At the end of the quantification, it was reported by the tool that the estimated average fragment length is zero. When I look at the output abundance file, I have quantification TPM values which are not zero. So, I hope there is no p ...
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Comment: C: Script: Downloading fastq files from ENA database
... Thanks for the input. ...
written 5 weeks ago by jayeshkumarsundaram0
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Comment: C: Script: Getting information about SRX experiment ID from NCBI database
... Thanks! I added the usage information in the script as well ...
written 5 weeks ago by jayeshkumarsundaram0
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Comment: C: Script: Downloading fastq files from ENA database
... Just create the file "SRRs_to_process.txt" in the same directory as the script. The script will automatically read in the file. ...
written 5 weeks ago by jayeshkumarsundaram0
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Tool: Script: Getting information about SRX experiment ID from NCBI database
... The following is the link to the script: [Gist github link][1] Create a file named "list_of_all_srx.txt" in the same directory as the script file and this file should have a list of single SRX ID as entries in every line. Script also generates an output file named "list_of_all_srx_with_info_on_seq ...
next-gen blog tool rna-seq written 5 weeks ago by jayeshkumarsundaram0
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Tool: Script: Downloading fastq files from ENA database
... Script for downloading fastq files from ENA database: [Gist github link][1] Create a file named "SRRs_to_process.txt" in the same directory as the script file and this file should have a list of single SRR ID as entries in every line. Fastq files will be downloaded in the same directory where the ...
next-gen tool rna-seq sequencing written 5 weeks ago by jayeshkumarsundaram0
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Answer: A: Masking and Parsing problem in Standalone BLAST 2.7.1?
... Can you try using -mask_data ‘XYZ_dust.asnb,XYZ_mask.asnb’ ...
written 6 months ago by jayeshkumarsundaram0
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Comment: A: Turn Off Blast Search On Reverse Complement Strand In Blastn
... I think you should someone take care of the target or subject strandedness as well. You should post - filter the results based on the alignment location I guess in query and subject/ target ...
written 6 months ago by jayeshkumarsundaram0
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Comment: A: Paired-End Data Only Has One Read Per Spot
... https://www.biostars.org/p/348888/ Did you find out why? ...
written 2.3 years ago by jayeshkumarsundaram0

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