User: Ammu

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Ammu0
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Posts by Ammu

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Stringtie output for DGE
... Yes, I have the ctab files as the output. So does the option -e mean only for transcript annotated in the reference genome? ...
written 1 day ago by Ammu0
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Stringtie output for DGE
... I've coverage tables generated with StringTie using only the -B option. Can this be used as an input for Ballgown for DGE? PS: I haven't used the -e option. ...
stringtie ballgown written 1 day ago by Ammu0
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RNA-seq biological replicates for DGE
... I would like to know how you treat biological replicates for differential gene expression? So far, they have similar QC after trimming adapters and so I proceeded with alignment to reference genome, Now after the alignment I am not clear how to treat these biological replicates in the Differential g ...
rna-seq dge written 4 days ago by Ammu0 • updated 4 days ago by Devon Ryan73k
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Comment: C: BCFtools variant calling format
... bcftools view -bvcg B1_C.raw.bcf >B1_C.vcf I tried it.. it is still not generating a separate output file ...
written 5 days ago by Ammu0
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BCFtools variant calling format
... I run the command line below (as a job script on HPC): samtools mpileup -uf Ca_v1.0_kabuli_ref.fasta B1_C.bam bcftools view -bvcg B1_C.raw.bcf I find the output file is generated in the slurm-out (the HPC specific job run output file). I am not sure if I am going wrong with the script some ...
variant call rna-seq written 5 days ago by Ammu0 • updated 5 days ago by Ram12k
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Comment: C: StringTie's merge function
... This term of multiple samples is what I am not clear about. Does it mean the biological replicates or different genotypes ? In my case, I have biological replicates, different genotypes with different tretment to identify differential gene expression. ...
written 6 days ago by Ammu0
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StringTie's merge function
... Is the stringtie's merge used to merge the transcripts fronm biological replicates prior to differential expression analysis? ...
rna-seq written 8 days ago by Ammu0 • updated 6 days ago by Kevin Blighe6.7k
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Misamtch penalty in RNA-seq alignment
... I would like to know setting the mismatch parameter default in HISAT2 (-mp, Min=2, Max=6), what is the likelihood to miss a SNP in the region? ...
rna-seq hisat2 written 8 days ago by Ammu0 • updated 8 days ago by Istvan Albert ♦♦ 74k
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RNA-seq biological replicates
... I've got PE Illumina Hi-seq RNA-seq data. I trimmed the adapters and then aligned the reads to the reference genome. Now before proceeding towards transcript assembly and quantification, I would like to know how to screen down which of the three biological replicates should I take forward for furthe ...
rna-seq written 12 days ago by Ammu0 • updated 12 days ago by Kevin Blighe6.7k
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Comment: C: genome index file
... Yeah, the manual says so, but I came across a paper where they had generated large genome index for a ref genome of size 740 Mbp. I was trying to understand why they had done so? ...
written 13 days ago by Ammu0

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Scholar 14 days ago, created an answer that has been accepted. For A: RNA-seq read alignment

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