User: bhuwankhatri11

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Posts by bhuwankhatri11

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Comment: C: Compare between two columns of two different files and print common
... Hi Kevin, It worked! I am new to awk. Could you please explain how this code works? Thanks. ...
written 3 days ago by bhuwankhatri1110
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Comment: C: Compare between two columns of two different files and print common
... I tried matching $5 of file1 with $6 of file2, but it didn't work. awk 'NR==FNR{a[$5]=$1;next}a[$6]{print $0 "\t" a[$6]}' file1 file2 >outfile ...
written 3 days ago by bhuwankhatri1110
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Compare between two columns of two different files and print common
... Hi I have two files, File1 Chr1 NC_029516.1 19961 - LRRC16B Chr1 NC_029516.1 23408 - LOC107314597 Chr1 NC_029516.1 31174 + LOC107305688 Chr1 NC_029516.1 156107 - ACR Chr1 NC_029516.1 193750 + LOC107319936 Chr1 NC_029516.1 457876 + SHANK3 Chr1 NC_029516.1 549801 - DENND ...
awk bash written 3 days ago by bhuwankhatri1110 • updated 3 days ago by pfs90
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Comment: C: Extract gene lists using two files
... Thank You Alex Reynolds! I worked now. I appreciate your help. ...
written 3 days ago by bhuwankhatri1110
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Comment: A: Extract gene lists using two files
... I removed headers of both of the files using sed command: `sed '1d' file1.txt` File1 becomes like this: deletion chr10:742501-778500 36000 0.654632 5.86769E-05 4097.15 0.00078794 12578 0.0298329 1.30923 deletion chr10:1726501-1755000 28500 0. ...
written 3 days ago by bhuwankhatri1110
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Comment: C: Extract gene lists using two files
... Second bed looks like: Chrom End Strand Accession Start Gene_Name Chr1 5379 - NC_029516.1 967 RNF212B Chr1 19961 - NC_029516.1 5341 LRRC16B Chr1 23408 - NC_029516.1 20428 LOC107314597 Chr1 31174 + ...
written 3 days ago by bhuwankhatri1110
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Comment: C: Extract gene lists using two files
... Hi Pierre, Thank you for your reply. Now I am able to create both the bed files. Which command line of bedtools will you suggest for the result? ...
written 3 days ago by bhuwankhatri1110
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Comment: C: Extract gene lists using two files
... Hi Alex, The second command line produced error like this: awk -v OFS="\t" '{ print $1, $4, $5, $2, $3, $6, $7; }' second.txt | sort-bed - > second.bed Non-numeric start coordinate. See line 1 in -. (remember that chromosome names should not contain spaces.) ...
written 3 days ago by bhuwankhatri1110
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Extract gene lists using two files
... Hi, I have two files with file1 having coordinates of genes and file2 containing list of genes. How can I extract genes lists from file2 using coordinates from file1? File1: **CNV_type Coordinates size val1 val2 val3 val4 val5 val6 cp** deletion chr10:1726501-1755000 28500 0.586226 9.73 ...
shell script unix awk written 4 days ago by bhuwankhatri1110
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VISUALIZING SPECIFIED REGIONS using CNVnator
... How can we visualize specified regions using CNVnator? Is there any way besides ssh -X user@host method? Thanks, ...
cnv written 7 days ago by bhuwankhatri1110

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