User: cpad0112
cpad0112 • 10k
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Posts by cpad0112
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Comment:
C: Pipelines and pseudocodes
... Refer to tips and tricks on trimming ngs data online. ...
written 6 hours ago by
cpad0112 • 10k
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... Try:
samtools view -F 2304
relevant samflags:
not primary alignment (0x100)
supplementary alignment (0x800) ...
written 1 day ago by
cpad0112 • 10k
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... try reinstalling affy library and see if the issue goes away. ...
written 1 day ago by
cpad0112 • 10k
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... not fastq, it is fastg (updated the post). Spades outputs contigs for each kmer. With higher Kmer, contig number goes down. But the relevancy of such assembly is in question. For that reason, you may need to use software like bandage or quast/ICARUS to identify the relevant assembly ...
written 1 day ago by
cpad0112 • 10k
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... did you have a look at fastg files and the number of contigs for each kmer? You can also check how good your assembly with Bandage https://github.com/rrwick/Bandage. https://www.biostars.org/u/27586/ ...
written 1 day ago by
cpad0112 • 10k
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... It seems you have used several k-mer sizes. Is the contig number same across all the K-mer sizes? https://www.biostars.org/u/27586/ ...
written 1 day ago by
cpad0112 • 10k
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... with awk and sed:
$ sed -nr '/CHROM|mis|\tsyn/p' test.txt
CHROM_POS ANN Annotation
CM009840.1_4421500 A|missense_variant|MODERATE|LOC102415844|gene14 |1/1|c.298C>T|p.Ar|| missense
CM009840.1_4421553 A|missense_variant|MODERATE|LOC102415844|gene14|transcript|rna37|p || misse ...
written 1 day ago by
cpad0112 • 10k
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... This tutorial is very useful https://www.biostars.org/u/27586/, however code and image need revisiting. ...
written 1 day ago by
cpad0112 • 10k
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... Could you provide example data for your query? ...
written 1 day ago by
cpad0112 • 10k
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... .tabular file is a tab separated values (.txt). Take a back up of .tabular file, change the extension of existing file to .tsv or .txt and then try opening with excel. One has option to change the output while using featurecounts using `-o output.txt`. I guess you are in windows, try using softwar ...
written 1 day ago by
cpad0112 • 10k
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For C: can someone read this result to me
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