User: v.shapovalova1

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Posts by v.shapovalova1

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Comment: C: sequencing depth vs quality assembly
... Thank you very much! seems that it's what I'm looking for. am i right that it'll removereads with the same indexes from formard file and reverse file? ...
written 7 days ago by v.shapovalova10
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Comment: C: sequencing depth vs quality assembly
... Yes. I'd like to check the assembly with lower amount of reads. But i suppose that the indexes from forward and reverse should be the same. like in this post: https://www.biostars.org/p/6544/ ...
written 7 days ago by v.shapovalova10
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Comment: C: sequencing depth vs quality assembly
... I suppose that i need the same reads for forwars and reverse for assembly. So i need to take indexes. No? ...
written 7 days ago by v.shapovalova10
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sequencing depth vs quality assembly
... Hello, I have paired-end Illumina reads, now the depth of sequencing is 100x and I've found the plasmid consisted of one full-length contig. I'd like to check if depth 50x is good enough for my aims. How could I do it? A lot of thanks, Valery ...
assembly quality written 8 days ago by v.shapovalova10 • updated 8 days ago by Mensur Dlakic5.4k
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Rearrange contigs to start with repA
... Hello, I have a contig with replicon of plasmid. I'd like to make the contig starts from repA. How could I do it? A lot of thanks, Valery ...
assembly plasmid written 10 days ago by v.shapovalova10
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BRIG output not only pictures
... Hello, I'd like to compare the contig(I suppose it's a circular plasmid) with the best matches from blast. I used BRIG tool for this and it made me very good pictures. But now I'm interested in coordinates of difference. Where I could take this information? I have SCRATCH folder after BRIG with a ...
assembly alignment brig written 18 days ago by v.shapovalova10
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Comment: C: Flagstat vs stats Samtools
... Thank you for your explanation, seems that at last I understood. I have 2 mln entries /lines in the bam file and 632 thousands are for primary alignment, 1,4 mln for secondary and 13 thousands for supplementary. -F 2304 gives me 623141. so 9799(632.940 primary alignments) entries are out of this sub ...
written 5 months ago by v.shapovalova10
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Comment: C: Flagstat vs stats Samtools
... 2081062 - 1434239 - 13883 = 632940 are these numbers for # of alignments but not reads, right? so for 632940 reads I have total 2.081.062 alignments 1.430.239 alignments secondary 13.883 supp ...
written 5 months ago by v.shapovalova10
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Flagstat vs stats Samtools
... Hello, I have a bam file and the output of flagstat is **2081062 + 0 in total (QC-passed reads + QC-failed reads)** **1434239 + 0 secondary** 13883 + 0 supplementary 0 + 0 duplicates 2057380 + 0 mapped (98.86% : N/A) 0 + 0 paired in sequencing 0 + 0 read1 0 + 0 read2 ...
samtools rna-seq written 5 months ago by v.shapovalova10
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(Closed) RNA-seq from Nanopore featureCounts
... Hello, I have RNA-seq reads from Nanopore(kit RNA002, U-based fastq), I aligned them with minimap2 and tried to count with featureCounts. The reference was transcriptome from https://www.gencodegenes.org/human/. my command was fc<- Rsubread::featureCounts(files="aln.bam",annot.inbuilt="hg3 ...
software error R rna-seq sequencing written 6 months ago by v.shapovalova10 • updated 6 months ago by Devon Ryan95k

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