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User: seta

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seta • 970
Reputation:
970
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Sweden
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3 years, 6 months ago
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Posts by seta

<prev • 596 results • page 1 of 60 • next >
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Comment: C: Poly A trimming from RNA-seq data by bbduk (bbmap package)
... Thanks. Sorry, how to find out which strand was sequenced? data obtained by Illumina TruSeq™ RNA Sample Preparation Kit. I just see a part of sequencing reads and don't see AAAA or TTT. However, mRNA was purified from total RNA using poly-T oligo-linked magnetic beads, so there is a probable AAA/TTT ...
written 4 hours ago by seta • 970
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Poly A trimming from RNA-seq data by bbduk (bbmap package)
... Hi all friends, For trimming polyA tail from RNA-seq data using bbduk, I found two flags: `"trimpolya=10”`, which trim leading or trailing sequences of at least 10 A or T and `“literal=AAAAA”` along with adjusting the value of k= as needed. I tried `“trimpolya=10`”, but faced the error, seemingly, ...
polya trimming bbduk bbmap rna-seq written 13 hours ago by seta • 970 • updated 12 hours ago by WouterDeCoster ♦ 28k
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Comment: C: Is haplotype phasing essential after variant calling?
... Thank you very much for your nice explanation. The initial variant analysis showed that there is the high rate of variation in our data (that is from a given population) in comparison to the human reference genome, so reference genome or HapMap cannot be used for haplotype phasing, yes? Could you pl ...
written 7 days ago by seta • 970
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Is haplotype phasing essential after variant calling?
... Hi everybody, Sorry if you find the question is basic for you. I want to determine variants of human blood groups genes from whole genome sequencing data of a given population. I read some about the haplotype phasing, but I'm not sure if it is essential after variant calling in my work? Could you p ...
genome sequencing haplotype phasing written 8 days ago by seta • 970 • updated 8 days ago by WouterDeCoster ♦ 28k
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Comment: C: Aligning short reads to a human specific gene instead of reference genome
... Thanks for your explanation... so, I go ahead with the reference genome. ...
written 14 days ago by seta • 970
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Comment: C: Aligning short reads to a human specific gene instead of reference genome
... Thanks, the reads came from the whole genome sequencing. I read that aligning reads to the specific gene may be better resolve homologous genes, but I'm not sure about the correctness. Please kindly let me know what do you think? ...
written 14 days ago by seta • 970
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Aligning short reads to a human specific gene instead of reference genome
... Hi all, My focus of study is on the two human homologous genes related to blood groups, which have also hybrid forms due to gene-rearrangement. I'm going to detect various polymorphisms within them. I'm thinking of aligning short reads (PE, 100bp) to these reference genes from GenBank instead of th ...
human reference genome alignment written 14 days ago by seta • 970
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Comment: C: Please suggest your idea for variant calling analysis of many BAM files from who
... Thanks, looking for germline variant. ...
written 17 days ago by seta • 970
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Comment: C: Please suggest your idea for variant calling analysis of many BAM files from who
... Many thanks for your nice explanations. However, working with cohort can be more difficult than the single genome. Could you please kindly let me know if there is any workflow/pipeline for handling and parsing of a cohort WGS analysis? ...
written 17 days ago by seta • 970
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Please suggest your idea for variant calling analysis of many BAM files from whole genome sequencing
... Hi all, I have the information of whole-genome sequencing (BAM files) of about 1100 individuals (human) that should be processed to find all variants of specific genes. I read and browsed a lot, however as it’s my first experience in this filed, I haven’t obtained a final conclusion. Could you plea ...
variant calling alingnment whole genome sequencing written 18 days ago by seta • 970 • updated 18 days ago by finswimmer • 2.0k

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