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Why difference in Hisat2 and bamqc from qualimap results?

bamqc qualimap rna-seq hisat2 written 9 days ago by Bioinfo • 170 • updated 9 days ago by Biostar ♦♦ 20

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understanding contig statistics

assembly mapping reads qualimap coverage spades written 14 months ago by mary • 0 • updated 14 months ago by Brian Bushnell ♦ 15k

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504

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Abnormal coverage profile

quality qualimap rna-seq rna degradation written 21 months ago by Gary • 440

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1.2k

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Qualimap result interpretation

qualimap written 3.4 years ago by Aura • 0 • updated 3.4 years ago by Antonio R. Franco • 3.6k

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Recent Replies

C: RefSeq transcripts *.rna.fna.gz files by Kevin Blighe ♦ 17k
From what I can tell, the files in the directory ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/anno...
C: Aligning Ion torrent sequenced genome with a reference sequence by genomax ♦ 46k
Can you post output of `head -12 your_sequence_file`?
C: RNA seq sample reads don't map by Devon Ryan ♦ 78k
Can you post a couple example reads from the highly problematic sample? What sequencer were these...
A: Strategy in WGS variant calling using GATK (CombineGVCF step) by vdauwera • 680
A simpler way of using a list of contigs or intervals to restrict analysis to areas of interest i...
C: Surrogate variable analysis: ask for a practical example by jonellevillar • 0
Hi Andrew, Thank you for your comments and explanations. I have limited experience using the SVA ...
C: Theory v Reality by d-cameron • 1.5k
>So for this protein the numerical result from the allele analysis will be "weaker" than that ...
C: Aligning Ion torrent sequenced genome with a reference sequence by Paul • 50
@Bastein, I have updated the post now, to make it more clear, Do i need specific ion torrent mapp...
C: Aligning Ion torrent sequenced genome with a reference sequence by Bastien Hervé • 650
You didn't specify the output : > [-S ]
C: Aligning Ion torrent sequenced genome with a reference sequence by Bastien Hervé • 650
What was the output of the `bowtie2-build genome.fasta genome_index` ? Did it end successfully ? ...
C: Theory v Reality by urema • 0
Thanks for the reply, One of the toy problems I am trying to replicate in the real world, with r...
A: Nomenclature in HGVS by mkamranazim • 0
Thanks very much for help. Kamran
A: extracting sequence from fast file by JJ • 220
Check out the [gffread][1] utility. gffread can be used to generate a FASTA file with the DNA seq...

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