User: Sureshkumar V.

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Posts by Sureshkumar V.

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Comment: C: Fastq_quality_filter: found invalid nucleotide sequence
... Ok, egeulgen, I will try and let you know. ...
written 6 months ago by Sureshkumar V.0
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Fastq_quality_filter: found invalid nucleotide sequence
... I am trying to filter reads(Illumina data - RNA-Seq) based on the quality of 30 using the fastx toolkit. But I got an error like this. fastq_quality_filter: found invalid nucleotide sequence (GCGGAGWAACCGTTCGGCEACCAGGTGGCATCGCCGCCGAGGGWGCTCCCGTGGCGCGGGCAGTCGTTGACGAACATCTC) on line 85766. How to re ...
assembly ngs rna-seq written 6 months ago by Sureshkumar V.0 • updated 6 months ago by Sej Modha3.6k
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Comment: C: Pileup file error
... Sir, When I saw using IGV. The Variant Positions has mapped to reads. I followed your parameters to make pileup file. I got the result, but It shows 0 reads in the position. Why does it show like this? ...
written 7 months ago by Sureshkumar V.0
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Pileup file error
... Hi, I am working on the genome assembly. A sequence length 1216bp. Reads fully mapped on that region. When I am creating pileup file using samtools, I got only 1034bp. How to clarify this problem? Thanks in advance ...
assembly ngs snp written 7 months ago by Sureshkumar V.0 • updated 7 months ago by Devon Ryan84k
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How to create consensus from bam file without IUPAC code?
... Hello, I am working in Genome assembly(Reference Guided), I want to create consensus sequence from bam file.I tried bcftools and vcf-consensus. But, I got some IUPAC code. I want consensus sequence without IUPAC Code. Reads: ATGC**A**TGCATGC ATGC**G**TGCATGC ATGC**A**TGCATGC Consensus: ATGC**R ...
genome assembly sequence written 9 months ago by Sureshkumar V.0 • updated 9 months ago by toralmanvar530

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