User: johnnytam100

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johnnytam10010
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Posts by johnnytam100

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Fermikit : Any recommendation on visualization of the output files?
... I have completed the unitig building and read-mapping using fermikit to discover if any indels are present in my reference sequence. Does anyone have experience on how to visualize the mapping results using the various output files from fermikit? Thank you very much! ...
indel fermikit vcf visualization bam written 8 days ago by johnnytam10010
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Transposable element (TE) of plants, how conserved and options for blastn?
... I am now searching for the position of transposable elements (TE) in the assembled whole-genome contigs of persimmon fruit (Diospyros Kaki). Since there is not a transposable element database of such a species so rare of research interest, I have to use TE database from other plants (e.g. MIPS Plan ...
te transposable element blastn written 9 days ago by johnnytam10010
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Pindel during compile : pindel.h:35:24: error: htslib/sam.h: No such file or directory
... When I tried to [compile][1] Pindel using the following command : ./INSTALL /data/tam/script/samtools-1.5/ The following error (partially) appeared : pindel.h:34:26: error: htslib/khash.h: No such file or directory pindel.h:35:24: error: htslib/sam.h: No such file or directory In ...
pindel htslib written 10 days ago by johnnytam10010 • updated 10 days ago by Pierre Lindenbaum98k
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Breakdancer : samtools pid process 7845 is still there... invoking kill -9 on 7845 ... Closing samtools process : 7845
... My command : ../../script/breakdancer-test-compile/lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl libextract-TTN_1aTTN_mapped_read_aln.sorted.bam This error appeared : > Processing bam: libextract-TTN_1aTTN_mapped_read_aln.sorted.bam > Closing BAM file > Send TE ...
7845 breakdancer samtools kill written 10 days ago by johnnytam10010
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Comment: C: Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run
... It worked!!! Thank you very much!!! ...
written 10 days ago by johnnytam10010
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Comment: C: Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run
... I tried... and the result is No module found for "Statistics::Descriptive". And I am trying to install Statistics-Descriptive-3.0612 now but another error said I don't have permission to write... ERROR: Can't create '/usr/local/share/man/man3' Do not have write permissions on '/usr/l ...
written 12 days ago by johnnytam10010
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Breakdancer : Can't locate Statistics/Descriptive.pm in @INC while trying to run bam2cfg.pl
... My command is as follows : /data/tam/script/breakdancer-test-compile/lib/breakdancer-max1.4.5-unstable-66-4e44b43/bam2cfg.pl bwa1/bam/TTNR_bam_0-1000/libTTNRgenome_master_aln.bam.tmp.0000.bam However, the error as follows appeared : Can't locate Statistics/Descriptive.pm in @INC (@INC con ...
perl breakdancer bam2cfg.pl inc written 13 days ago by johnnytam10010 • updated 12 days ago by amy.bashir50

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