User: deepti1rao

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Posts by deepti1rao

<prev • 71 results • page 1 of 8 • next >
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Comment: C: What Are You Using For A Reference Assembler?
... How can we have the snps and Indel replaced, and have the uncovered regions of the genome, represented as a series of Ns in the consensus assembly? ...
written 25 days ago by deepti1rao0
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Comment: C: Is there a way to reformat vcf 4.2 down to 4.1?
... How does one execute this script? ...
written 28 days ago by deepti1rao0
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Finding genes/proteins from variant files
... After getting a variant file and using a software like VEP or snpEff to annotate variants, I want to look up ensembl for validating the presence of frameshift variants that may be contributing towards a phenotype. Instead of studying each predicted variant manually, by checking if a locus has a gene ...
annotation variants written 6 weeks ago by deepti1rao0
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Error value for safely scaffolding contigs with SSPACE
... ![insert size histogram][1] [1]: https://ibb.co/kALZGJ Please find the insert size histogram, plotted using picard tool. ## METRICS CLASS picard.analysis.InsertSizeMetrics MEDIAN_INSERT_SIZE MODE_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_D ...
assembly sspace insert size read pairs error written 8 weeks ago by deepti1rao0
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Using the same read library to scaffold read tracked contigs
... I have used Velvet to assemble reads into contigs with `-scaffolding no` and `-read trkg yes`. Now that read tracking is already done, does it make sense to run the contigs through a scaffolder with the same read library? As per velvet's stdout, 280699288/441647786 reads have been used in the assemb ...
reads scaffolding velvet written 9 weeks ago by deepti1rao0 • updated 9 weeks ago by toralmanvar420
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Comment: C: SSPACE for scaffolding
... Yes, these are "real", generated using Velvet with the --no scaffolding option. ...
written 9 weeks ago by deepti1rao0
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Comment: A: SSPACE for scaffolding
... Can someone help with this? ...
written 9 weeks ago by deepti1rao0
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SSPACE for scaffolding
... I want to use a paired end library for scaffolding my contigs. I used the following command to estimate insert size using bbmap: bbmap.sh ref=reference.fasta in1=read1.fq in2=read2.fq ihist=ihist_mapping.txt out=mapped.sam #Mean 352.766 #Median 301 #Mode 271 #STDev 933.708 ...
contigs sspace insert size bbmap scaffolding written 10 weeks ago by deepti1rao0 • updated 9 weeks ago by Ram15k
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Comment: C: Continuous alignment of contigs with reference using blast /blat
... I do not intend to do a forced alignment. Also, I do not want to lose information by having my contigs soft clipped. I want to compare the contigs as a whole with the reference. That way, I may be able to annotate the draft genome and locate missassemblies/ structural variants that can be studied fu ...
written 10 weeks ago by deepti1rao0
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SOAPdenovo statistics output for Nx
... Here's the Nx output that I have got on running SOAPdenovo. Does column 2 represent L50 and column 3 N50?? Please clarify. N10 2252 11403 N20 1611 29595 N30 1239 53911 N40 982 84988 N50 781 124052 N60 621 173134 N70 489 235218 N80 382 314436 N90 196 ...
n50 soapdenovo assembly nx l50 written 10 weeks ago by deepti1rao0 • updated 25 days ago by toralmanvar420

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