User: saripalligautam86

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Posts by saripalligautam86

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Answer: A: CpG density in MEDIPS
... Thanks Lukas. In that case, can you please let me know what those bam counts actually indicate and how is the log fold change actually calculated using MEDIPS.meth? Regards, ...
written 3 hours ago by saripalligautam8610
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CpG density in MEDIPS
... Dear All, I am analyzing CpG coverage/density in wheat samples using the MEDIPS package. However, due to some technical reasons, I could not calculate CpG density using the coupling set function of MeDIPS. Although I am trying to do it by making some changes.   I would like to know that instead o ...
medips cpg written 10 hours ago by saripalligautam8610
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Comment: C: Indexing large chromosomes (like wheat) bam files in Rsamtools
... Thanks for your responses. Below is the output which I receive when I try to analyse CpG density using CS code of MEDIPS. Similarly, instead of MEDIPS, when I use QSEA, i get the output error that the index is not found and hence the process terminates. Anyways, since, Martin has replied that Rsamto ...
written 1 day ago by saripalligautam8610
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Indexing large chromosomes (like wheat) bam files in Rsamtools
... Hello All,   Is there a possible way to index bam files for large chromosomes(like wheat) using Rsamtools? Like in case of samtools using linux, .CSI (coordinate sorted index) is possible whereby .bam files for large chromosomes can be indexed. However, the .CSI index generated using samtools (thro ...
rsamtools csi index wheat written 1 day ago by saripalligautam8610
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Indexing large chromosomes (like wheat) bam files in Rsamtools
... Hello all,   Is there a possible way to index bam files for large chromosomes(like wheat) using Rsamtools? Like in case of samtools using linux, .CSI (coordinate sorted index) is possible whereby .bam files for large chromosomes can be indexed. However, the .CSI index generated using samtools (thr ...
rsamtools medips qsea written 2 days ago by saripalligautam8610
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Answer: A: Coupling set error in MEDIPS
... Thanks Lukas.   I will try QSEA package as suggested.However, could you point out a possible reason for the error which I encountered during coupling set function?Why the process stopped at reaching to chromosome 7?Do, I need to worry about this or proceed further with my analysis?   Regards, ...
written 4 days ago by saripalligautam8610
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Comment: C: Coupling set error in MEDIPS
... Thanks Lukas.   I will try QSEA package as suggested.However, could you point out a possible reason for the error which I encountered during coupling set function?Why the process stopped at reaching to chromosome 7?Do, I need to worry about this or proceed further with my analysis?   Regards, ...
written 5 days ago by saripalligautam8610
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Coupling set error in MEDIPS
... Dear All,   I am tring to analyse my MeDIP-Seq data in wheat using MEDIPS package. For this purpose, as mentioned in my earlier post, I created .2bit file from .fasta whole genome sequence file and then I created a forge bsgenome package and then build the package using devtools in R. I created me ...
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CouplingSet error in MeDIPS
... Dear All,   I am tring to analyse my MeDIP-Seq data in wheat using MEDIPS package. For this purpose, as mentioned in my earlier post, I created .2bit file from .fasta whole genome sequence file and then I created a forge bsgenome package and then build the package using devtools in R. I created me ...
medips coupling set error written 6 days ago by saripalligautam8610
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converting a fasta file to .2bit format
... Dear All,   I am using biostrings and rtracklayer to convert a wheat reference sequence which is a fasta file to a .2bit file in order to use it for BS forgenomepackage. I first used biostrings to get a DNAStringSet, the output is shown below: > Biostrings::readDNAStringSet("wheatreference.fas ...
biostrings rtracklayer written 8 days ago by saripalligautam8610 • updated 8 days ago by Hervé Pagès ♦♦ 13k

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