User: mks002

gravatar for mks002
mks002100
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Location:
Bangalore. India
Last seen:
5 days, 4 hours ago
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2 years ago
Email:
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Posts by mks002

<prev • 57 results • page 1 of 6 • next >
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Masurca Assembler for 450 mb genome
... Hello all, I have started the assembly with Short insert and Long insert and Mate pair reads with 100X genome coverage. It has taken around 1.5 Tb ram and running from past one day. There is no issue with space. Kmer i have given as "auto" so its running with 31 kmer and work2.1 files are genera ...
genome assembly ngs next-gen written 16 days ago by mks002100
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Comment: C: Goat Genome gene prediction
... Hello, I took little time but the gff was generated, Below is the look of my gff i used -g option for pulling out the gff. ##gff-version 3 ### ### Scaffold_21964|length1264 maker gene 741 1212 . + . ID=maker-Scaffold_21964|length1264-exonerate_pr ...
written 7 weeks ago by mks002100
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Comment: C: Goat Genome gene prediction
... Hello, My maker run is over Below is the Output `Start_time: 1509976900 End_time: 1511273877 Elapsed: 1296977` Not able to merge the gff. Can u help me out. ...
written 8 weeks ago by mks002100
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Comment: C: Goat Genome gene prediction
... Hello, I think that maker is now on final step. Below is the out put what i m seeing. cleaning blastx... in cluster::shadow_cluster... ...finished clustering. in cluster::shadow_cluster... ...finished clustering. cleaning clusters.... total clusters:37 now processing 0 ...
written 8 weeks ago by mks002100
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Finding lysogenic gene in phage
... Hello all, can one suggest what would the possible approach for finding out the lysogenic gene, since we have identified the lytic gene. Can any one tell the factors to be considered for lysogenic property study in the genome. ...
genome assembly next-gen gene sequencing written 8 weeks ago by mks002100
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Comment: C: Goat Genome gene prediction
... Hello Puli, Maker i started and it is running from past 12 days. Why its taking so much time ? ( 12 threads i had given ) It created around 254 folders and each folders has > 100 subfolders. Total of > 35000 folders for each scaffold i guess. I have around ~3gb genome and ~45k scaffolds. I ...
written 8 weeks ago by mks002100
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Comment: C: Goat Genome gene prediction
... I have >100Mb some 10 scaffolds. And picking one one gene would not be feasible i think need to rework some other way. ...
written 9 weeks ago by mks002100
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Comment: C: Goat Genome gene prediction
... Now since Augustus gene models are already there can we go ahead with training steps. Since Genome size ~3 gb it is quite time taking to go through all the processes. Can we do one step of training the augustus and work on it. Artemis loading this big genome also is great trouble (error in loadin ...
written 9 weeks ago by mks002100
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Comment: C: Goat Genome gene prediction
... For Artemis which bam file to upload since no alignment was performed. For this assembly Rna-seq data is not available. So we can go ahead ? what would be feasible solution. ...
written 10 weeks ago by mks002100
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Comment: C: Goat Genome gene prediction
... Hello , Thank you for your extended help. The results have been compared and observed stats as below ---------- Description -------------1st column (sample goat)----------2nd column (ref goat) ---------- Gene All stats ---------- Count ...
written 10 weeks ago by mks002100

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