User: AW

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AW350
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350
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United Kingdom
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1 year, 11 months ago
Joined:
6 years, 12 months ago
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a**************@ucl.ac.uk

about me

Posts by AW

<prev • 80 results • page 1 of 8 • next >
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Answer: A: RSEM ignores quality scores?
... Response from Bo Li Hi Alison, RSEM does not ignore quality scores. It uses the quality scores to help it allocate multi-mapping reads. But when RSEM calls Bowtie2, we set the Bowtie2 parameters in a way that ignores quality scores. In particular, we set '--mp 1,1', which implies a mismatch pe ...
written 2.0 years ago by AW350
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RSEM ignores quality scores?
... Dear all, I want to quantify gene expression for my Trinity transcriptome assembly using RSEM. I am getting confusing results depending on how I specify quality scores of the Illumina paired end reads. They are Illumina 1.5 and have phred 64 quality scores. The RSEM manual says that phred+33 is de ...
phred rsem written 2.0 years ago by AW350
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Varscan mpileup2snp coverage filter
... Dear all, Does anyone know what the --min-coverage threshold in mpileup2snp is filtering on? Is it DP= Quality Read Depth of bases with Phred score >= 20 or SDP= Raw Read Depth as reported by SAMtools? Thanks ...
mpileup2snp varscan written 2.8 years ago by AW350
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Varscan mpileup2snp parameters
... Dear all, I wish to use mpileup2snp to call SNPs. I am confused by two of the parameters --min-var-freq NUM A decimal value indicating the minimum VAF for calling variants. For individual samples, 0.20 to allow for variant under-representation. Lower for pooled samples (maybe ½ the expected freque ...
mpileup2snp varscan snpcalling written 2.8 years ago by AW350
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VCFtools filter - genotype quality score changes
... Hi, I ran the following filtering command vcftools --vcf test.vcf --out test.test.vcf --remove-indels --remove-filtered-all --max-alleles 2 --max-alleles 2 --recode --recode-INFO-all However, when I compare the new `test.test.vcf` compared to the original `test.vcf` the `GQ` scores of some s ...
genotype quality gq vcftools written 2.9 years ago by AW350 • updated 2.9 years ago by Brice Sarver2.8k
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How to do consensus calling from bam files
... Hi, I want to extract consensus sequences for a number of bam files with the intent to align sequences across individuals and build trees. I am following the advice here https://github.com/samtools/bcftools/wiki/HOWTOs via vcf2fq: samtools mpileup -uf ref.fa aln.bam | bcftools call -c | vcfutils.p ...
samtools snps bcftools consensus calling written 2.9 years ago by AW350 • updated 2.9 years ago by Brice Sarver2.8k
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Answer: A: HISAT - Stringtie
... Found the answer to the second question. I was using HISAT but StringTie developers recommend using HISAT2. In HISAT2 there is an option --dta/--downstream-transcriptome-assembly Report alignments tailored for transcript assemblers including StringTie. With this option, HISAT2 requires longer anchor ...
written 3.3 years ago by AW350
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Comment: C: HISAT - Stringtie
... Hi, Thanks for your comment! Yes I have read the paper. But it doesn't answer these questions, mainly because in the paper they use the output of Tophat2 as the input of StringTie. Tophat2 only reports one alignment per reads. ...
written 3.3 years ago by AW350
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HISAT - Stringtie
... I want to use the HISAT-Stringtie approach to quantify expression for my paired-end Illumina RNA-seq data. I see that by default HISAT reports up to 5 alignments for each read. “Default mode: search for one or more alignments, report each. k -5” If there are multiple alignments for a given read in ...
rna-seq written 3.3 years ago by AW350
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varscan2 mpileup2snp output contains indels
... Hi all, I ran varscan2 mpileup2snp but I see that the vcf output file contains indels? Record(CHROM=TR1087|c2_g1_i4, POS=1195, REF=TAAAAAAAAA, ALT=[AAAAAAAAAA, TA, T, TAAAA, TAAA, TAA, T]) Record(CHROM=TR669|c3_g1_i3, POS=3524, REF=CAAAA, ALT=[C, AAAAA, C, CAAAAA, C]) Record(CHROM=TR361|c2_g1_i1, ...
vcf indels mpileup2snp varscan written 3.4 years ago by AW350 • updated 2.5 years ago by Biostar ♦♦ 20

Latest awards to AW

Scholar 2.0 years ago, created an answer that has been accepted. For A: Bio.Phylo.Paml.Codeml'S Results Parser Quietly Fails To Read All The Data
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Bio.Phylo.Paml.Codeml'S Results Parser Quietly Fails To Read All The Data
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Extract consensus gene sequence (from gff file) from bam file
Popular Question 2.8 years ago, created a question with more than 1,000 views. For TMM normalisation from RSEM raw counts
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Bio.Phylo.Paml.Codeml'S Results Parser Quietly Fails To Read All The Data
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Mpileup Segmentation Fault
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Bowtie2 Reads that aligned concordantly exactly 1 time
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Cufflinks - Assigning Transcripts Or Exons
Popular Question 3.2 years ago, created a question with more than 1,000 views. For RNA-seq normalization: How to use TMM and rpkm() in EdgeR
Epic Question 3.3 years ago, created a question with more than 10,000 views. For RNA-seq normalization: How to use TMM and rpkm() in EdgeR
Popular Question 3.5 years ago, created a question with more than 1,000 views. For TMM normalisation from RSEM raw counts
Appreciated 4.3 years ago, created a post with more than 5 votes. For RNA-seq normalization: How to use TMM and rpkm() in EdgeR
Great Question 4.3 years ago, created a question with more than 5,000 views. For RNA-seq normalization: How to use TMM and rpkm() in EdgeR
Good Question 4.3 years ago, asked a question that was upvoted at least 5 times. For RNA-seq normalization: How to use TMM and rpkm() in EdgeR
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Cufflinks - Assigning Transcripts Or Exons
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Mpileup Segmentation Fault
Scholar 4.5 years ago, created an answer that has been accepted. For A: Bio.Phylo.Paml.Codeml'S Results Parser Quietly Fails To Read All The Data
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Tophat 2 - Both Pairs Map Concordantly
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Mpileup Segmentation Fault
Student 4.9 years ago, asked a question with at least 3 up-votes. For RNA-seq normalization: How to use TMM and rpkm() in EdgeR
Popular Question 5.1 years ago, created a question with more than 1,000 views. For RNA-seq normalization: How to use TMM and rpkm() in EdgeR
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Tophat 2 - Both Pairs Map Concordantly

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