User: sophie.ehresmann

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Posts by sophie.ehresmann

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Comment: C: Htseq-count: discrepancy between raw count value and viewable value of reads on
... I went to look at the specific region, which is around 34,000 bp, for all of my samples. samtools view -o view_TBC_${SAMPLE}.tsv /gs/scratch/p1044860/Pipeline_output_SK_TBC/alignment/${SAMPLE}/${SAMPLE}.sorted.mdup.bam 16:2475051-2509560 For sample 1: 4402 total reads, of which only 1 is bad q ...
written 22 months ago by sophie.ehresmann10
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Htseq-count: discrepancy between raw count value and viewable value of reads on BAM with IGV
... Hello, I have aligned a trimmed FASTQ with STAR then sorted it and counted with htseq-count. When I look at the pos- sorted BAM on IGV for a specific gene, I get around 20 reads all over this gene for sample 1, 150 for sample 2, and 6000 for sample 3. However in the raw count read file, I see the s ...
htseq-count rna-seq written 22 months ago by sophie.ehresmann10 • updated 20 months ago by Biostar ♦♦ 20
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Discrepancy in DESeq2 fold change
... Hello, I am currently analysing RNA-Seq data obtained from Ion Proton. I have triplicates of all my samples, for an empty vector, a WT protein, and 3 mutants. I am having trouble understanding the DESeq2 results. When I compare my WT and my empty vector, in the raw counts I have gigantic differences ...
R deseq2 rna-seq written 2.5 years ago by sophie.ehresmann10 • updated 2.5 years ago by Santosh Anand5.0k

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