User: kspata

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kspata40
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1 year, 11 months ago
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Posts by kspata

<prev • 57 results • page 1 of 6 • next >
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Comment: C: Extracting contaminated reads from the sequenced data
... Hi Finswimmer, I observed that increasing the k-mer value decreases the number of matched reads. What should be the ideal k-mer size for paired reads of length 150bp. How will the interpretation of results related to matched reads will change with changing k-mer size? ...
written 10 days ago by kspata40
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Identify RNA and non-AAV vector molecules in a sample
... Hi, The sample used for sequencing was ssDNA viral particles sequenced on MiSeq PE250. The sample was initially mapped to a viral vector genome with a mapping rate more than 96%. **I wish to find what RNA molecules and non-AAV DNA molecules are present in the Sample.** So to achieve this the sample ...
assembly alignment contamination written 11 days ago by kspata40
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Audit trail for Bioinformatics software tools
... Hi, I analyze several samples every day for variant analysis using align to reference method. For this purpose I use different Bioinformatics software such as Bowtie2/BWA, Samtools, and Freebayes. Is there a way in which I can know which version of software was used to process a particular sample. ...
next-gen alignment samtools align written 14 days ago by kspata40 • updated 11 hours ago by Biostar ♦♦ 20
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Comment: C: PhiX forward and reverse reads for MiSeq and NextSeq Platform
... Thank You genomax!! I did contact Illumina, and was informed that the data is not available for NextSeq and MiSeq. I plan to use the data from the above links for validation. Which reference sequence should I use for mapping? I have found the following link: [https://www.ncbi.nlm.nih.gov/nucleotide/ ...
written 14 days ago by kspata40
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PhiX forward and reverse reads for MiSeq and NextSeq Platform
... Hi, I am in process of validating a pipeline for data pre-processing, align to reference and variant calling. I am interested in using the PhiX data from Basespace. But I can not find the raw sequence forward and reverse reads anywhere on Basespace. How can I obtain the Paired end data for both MiS ...
illumina next-gen sequencing written 17 days ago by kspata40
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Comment: C: Missing sequence from a cosmid de novo assembly
... It is present in the sample cosmid DNA as confirmed by PCR sequencing. But i guess it was either not sequenced or SPAdes failed to assemble. 1. Illumina sequencing failure can be confirmed by mapping forward and reverse reads to the missing DNA sequence which resulted in 0% mapping rate. ...
written 22 days ago by kspata40
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Comment: C: Missing sequence from a cosmid de novo assembly
... Thank you for replying. I performed further troubleshooting by searching for substrings of missing sequence in the contigs fasta file but did not find any match for substrings of length 50bp, 80bp, and 100bp. 1. What other assembly tools or strategies can I use to troubleshoot this? 2. Should I t ...
written 24 days ago by kspata40
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Comment: C: Error in parsing BAM file using readAlligned
... Thank you for replying. I tried using samtools command > samtools view Sample.bam "ref:6000-11000" > region.bam My original Sample.bam has `3264461` number of mapped reads and for the region.bam I got `3203443` number of reads. I think this command also includes the reads which overlap ou ...
written 4 weeks ago by kspata40
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Error in parsing BAM file using readAlligned
... Hi, I was trying to find number of reads within a specific target region. To perform this I found the post on Biostar [https://www.biostars.org/p/3407/#3414][1] [1]: https://www.biostars.org/p/3407/#3414 I installed the necessary packages into an R Studion session and performed the following c ...
gene R alignment written 4 weeks ago by kspata40 • updated 4 weeks ago by swbarnes24.7k
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Merge Samtools and Freebayes vcf files
... Hi, I am analyzing presence of variants in exonic regions of 10 genes. I have sequencing data for samples obtained from different individuals. I aligned the NextSeq PE 150 sequencing data to hg38 human genome assembly using `bowtie2` and called variants using `samtools` and `freebayes` and filtered ...
exome alignment variants written 5 weeks ago by kspata40 • updated 5 weeks ago by Pierre Lindenbaum116k

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