User: francois

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francois10
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6 days, 3 hours ago
Joined:
1 year, 7 months ago
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f*******@kroll.be

Posts by francois

<prev • 28 results • page 1 of 3 • next >
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Why do I have more reads in my .bam file than in my .fastq input file?
... I seem to have more reads after alignment than before. Before alignment ` awk '{s++}END{print s/4}' reads.fastq ` > 153265 After alignment `samtools flagstat align.bam` > 180051 + 0 in total (QC-passed reads + QC-failed reads) > 0 + 0 secondary > 26786 + 0 supplementary > 0 + 0 ...
fastq alignment bam written 6 days ago by francois10 • updated 6 days ago by Pierre Lindenbaum110k
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Can IGV tell me where to look?
... Hopefully that is a dumb question! I have Nanopore MinION reads from a (dirty) PCR and I am looking at my hg38-alignment on IGV. Can IGV somehow tell me where to look for reads/coverage? For example at the level of a chromosome. I do not understand how I am supposed to visually scan for reads/cove ...
minion nanopore igv written 13 days ago by francois10
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Comment: C: IGV not highlighting possible variants
... Did not seem to be the problem, but good to know, thank you. ...
written 22 days ago by francois10
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Answer: A: IGV not highlighting possible variants
... Thanks @WouterDeCoster. Just so we can close the post: I closed IGV, re-opened it and re-loaded `hg38` from the Menu in the top left. Seems to work now! ...
written 22 days ago by francois10
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Comment: C: IGV not highlighting possible variants
... I closed IGV, re-opened it and re-loaded hg38 and now it works. Who knows what went wrong... Thanks a lot! ...
written 22 days ago by francois10
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Comment: C: IGV not highlighting possible variants
... Ah, you are right! I did not notice it, but obviously that is linked to the problem. Any idea what is happening? I loaded hg38 directly from IGV... ...
written 22 days ago by francois10
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IGV not highlighting possible variants
... Surely this is trivial, but I have looked everywhere and I cannot find the answer... IGV sometimes does not want to highlight the possible variants in the coverage track (i.e. when it does the boxplot of the different allele frequencies). The problem does not come from the `Set allele frequency th ...
igv written 22 days ago by francois10 • updated 22 days ago by genomax51k
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Comment: C: Where are my reads in IGV?
... I am sorry, not sure I understand, why are you saying it is using a transcriptome reference? The website says: > The reference sequences are taken from the feature strand of the most > recent human genome assembly, GRCh38. ...
written 4 weeks ago by francois10
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Comment: C: Where are my reads in IGV?
... Here it is. `samtools idxstats sort.bam` A1BG 8322 0 0 A1CF 86267 0 0 A2M 48566 0 0 A2ML1 64530 0 0 A3GALT2 14333 0 0 A4GALT 29178 0 0 A4GNT 8670 0 0 AAAS 17409 0 0 AACS 77955 0 0 And so on. *PRNP*, which is the gene to which most of my reads should align ...
written 4 weeks ago by francois10
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Comment: C: "Invalid BAM file header: missing sequence name in file" when trying to visualis
... I created this reference myself, so it is whatever I called it: `grep ">" ref.fasta | head` > 106_46_amplicons_ref After that, the `.fasta` reference line is just a one line sequence of ~ 1k characters in lower case. And `samtools view align.sam | head` > 37d3e25f-875a-4cac-967a-b26d5 ...
written 4 weeks ago by francois10

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Scholar 22 days ago, created an answer that has been accepted. For A: IGV not highlighting possible variants

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