User: a.rex

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a.rex230
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Posts by a.rex

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TPM normalization factors in RNA-seq
... I have perhaps a naive question: In RNA-seq with Kallisto, est_counts are generated and TPMs per transcripts can be calculated. However, to compare between sample, sleuth is used to calculate between sample normalization factors. Therefore, TPM for the individual libraries need to be normalized to ...
rna-seq written 15 months ago by a.rex230
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Estimate Library Complexity Output Histogram - what do duplicate sets mean exactly?
... I have run this command on my bam file (it has already gone through MARKDUP): java -jar picard.jar EstimateLibraryComplexity INPUT=lib.bam OUTPUT=sample_libcomp.txt I get this output: ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMIN ...
picard alignment written 16 months ago by a.rex230
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How to interpret a short TLEN with 75bp PE seq?
... I have a pair of mapped reads that look like this: > SRR8441376.12918543 99 g4_3 1773574 45 40S25M10S = 1773574 25 CAGCGTGAGCGGTTCGCTGAAGTCCGGCCCCAGTTCGCACATTTCGGTGACGAACTGCAACACCCGGTCTTGTTC AAAAAEEEAEEEEEEEEEE6EEEEEEEEEEEEEEEEEEEEAEEEEEEAE SRR8441376.12918543 147 g4_3 1773574 45 26S25M ...
sequence alignment written 17 months ago by a.rex230 • updated 17 months ago by Pierre Lindenbaum129k
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Comment: C: Insert size of -20bp with ATAC-seq?
... I did not filter chrM as we do not have this information. ...
written 17 months ago by a.rex230
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Comment: C: Insert size of -20bp with ATAC-seq?
... It is very odd - it is for a obscure species and published a few days ago. ...
written 17 months ago by a.rex230
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Understanding 9th field of Bam file - insert size?
... I have a pair of reads that look like this: SRR8441376.13963941 69 g4_1 558410 0 * = 558410 0 GTATAATCTAATTGTTCATGATGGAATTCATATTGTTCAATTGCGTTATTATAATTACTTAGTTGCTTAATTTG AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEE ...
alignment sequencing written 17 months ago by a.rex230 • updated 17 months ago by ATpoint36k
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Comment: A: Insert size of -20bp with ATAC-seq?
... I realise now that perhaps a peak at 20bp (insert size) corresponds to a fragment of -95bp? ...
written 17 months ago by a.rex230
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Comment: C: Insert size of -20bp with ATAC-seq?
... I have uploaded said image now ...
written 17 months ago by a.rex230
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Insert size of ~20bp with ATAC-seq?
... I have recently downloaded some publicly available ATAC-seq data. I aligned with BWA to reference genome, removed duplicate (in this instance 70% of library is duplicates), and then used picardtools to generate a fragment size distribution. However, I see a large peak at around 20bp? The library was ...
alignment atac-seq sequencing written 17 months ago by a.rex230 • updated 17 months ago by ATpoint36k
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How can I use featurecounts after generating a bam file using BWA?
... I have a reference transcriptome, to which I have aligned reads using BWA. My goal is to quantify the aligned transcripts - how can I do this? Can I use featurescounts - bearing in mind that I have aligned to a transcript fa file. ...
features counts rna-seq written 18 months ago by a.rex230 • updated 18 months ago by h.mon30k

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Popular Question 17 months ago, created a question with more than 1,000 views. For Fetching NCBI ID for a list of species?
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Popular Question 21 months ago, created a question with more than 1,000 views. For Fetching NCBI ID for a list of species?
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Popular Question 22 months ago, created a question with more than 1,000 views. For Issues installing bcl2fastq?
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