User: saumya.sharma1509

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Posts by saumya.sharma1509

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Comment: C: i want to convert .ht2 files into FASTA file
... in command which file will be used? the original reference genome or .dict file or .fai file? ...
written 3 months ago by saumya.sharma15090
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Comment: C: i want to convert .ht2 files into FASTA file
... okayyy...can you please guide me any other way to find haplotypes? is there any way to obtain haplotypes from a vcf file? please provide me with the command for making ".dict file"? can you make me clear about the gatk command? I have to input ".dict file" "fai.file" while using the command or I ha ...
written 3 months ago by saumya.sharma15090
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Comment: A: i want to convert .ht2 files into FASTA file
... I have created a ".dict" file from picard tools. but then I have the error ...
written 3 months ago by saumya.sharma15090
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Comment: C: i want to convert .ht2 files into FASTA file
... it generates a ".fai" file but when I use that file on GATK it says not supported file format. ...
written 3 months ago by saumya.sharma15090
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Comment: C: i want to convert .ht2 files into FASTA file
... because GATK haplotypecaller needs fasta file of the indexed reference genome. if I am indexing my reference file again from samtools it says "not supported file format". so I think I need to convert the indexed files which I have obtained from hisat2 into FASTA file. if you could suggest any other ...
written 3 months ago by saumya.sharma15090
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i want to convert .ht2 files into FASTA file
... Hey, I want to convert .ht2 files into FASTA file. as I have obtained .ht2 files from Hisat2 tool and now I need to convert these files into fasta format please help? these .hts2 files are obtained as I have indexed my reference genome. now, I am calling haplotypecaller from GATK tools for haplotyp ...
fasta gatk tool hisat2 written 3 months ago by saumya.sharma15090
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Comment: A: can we replace #N/a with 0 for using edgeR
... we have fpkm values and obtained it from NCBI geoset ...
written 6 months ago by saumya.sharma15090
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can we replace #N/a with 0 for using edgeR
... hey I want to know that can I replace #N/A with the 0.it is an RNAseq data and I want to do the differential expression analysis in edgeR. can I replace #N/A with 0 ...
R rna-seq written 6 months ago by saumya.sharma15090
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Comment: C: error while making a DEGList object on R using edgeR package
... thankyou is there any way to convert FPKM data into read counts? ...
written 6 months ago by saumya.sharma15090
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error while making a DEGList object on R using edgeR package
... hey, I am doing an RNAseq analysis.(using edgeR) I am loading my data for differential analysis, my data is of normalized gene expression(FPKM). I am now just trying to make DEGList object but, it is showing "NA counts not allowed". I have removed all NA from the data and there is no blank cell in m ...
rna-seq edger written 6 months ago by saumya.sharma15090 • updated 6 months ago by WouterDeCoster40k

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