User: saripalligautam86

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Posts by saripalligautam86

<prev • 13 results • page 1 of 2 • next >
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All fragments/sequences captured using MeDIP are methylated?
... Dear All,   Could you please let me know whether all the sequences captured using MeDIP-Seq are methylated or does this also include some non-methylated fragments? If yes, does that mean that all the CGs or CG patterns identified from the MeDIP-seq data are methylated or is there a possibility of ...
methylation medip-seq cpgs written 4 weeks ago by saripalligautam8610
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Comment: C: Indexing large chromosomes (like wheat) bam files in Rsamtools
... Thanks Mike. As Herve Pages and you pointed out, I too believe that this is the error due to reference genome which I am using.I also tried other packages to count the number of CpGs in the reference genome (irrespective of .bam files); there too I am getting the similar type of error message.Now, ...
written 8 weeks ago by saripalligautam8610
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Comment: C: CpG density in MEDIPS
... Thanks Lukas, After reading the reference manual, I understand that .bam counts are the probable reads that are methylated (reads containing the methylated CpGs) if I am not wrong. You may please correct me if required. However, I am still confused what are the  logCPM values that are also returned ...
written 8 weeks ago by saripalligautam8610
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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 8 weeks 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 8 weeks 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 8 weeks 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 8 weeks 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 9 weeks 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 9 weeks 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 9 weeks ago by saripalligautam8610

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