User: Sureshkumar V.
Sureshkumar V. • 0
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Posts by Sureshkumar V.
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... Ok, egeulgen,
I will try and let you know. ...
written 18 months ago by
Sureshkumar V. • 0
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6 follow
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...
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 ...
written 18 months ago by
Sureshkumar V. • 0
• updated
18 months ago by
Sej Modha ♦ 4.4k
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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 19 months ago by
Sureshkumar V. • 0
0
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... 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 ...
written 19 months ago by
Sureshkumar V. • 0
• updated
19 months ago by
Devon Ryan ♦ 91k
3
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... 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 ...
written 21 months ago by
Sureshkumar V. • 0
• updated
8 months ago by
DNAngel • 30
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