User: lin.barnum

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lin.barnum230
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Posts by lin.barnum

<prev • 31 results • page 1 of 4 • next >
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Downloading Cds Fasta Sequences From Gene Ids
... I have a list of geneIDs obtained from UCSC genome browser like this: CG6854 CG8119 CG8359 CG9437 CpipJ_CPIJ001450 CpipJ_CPIJ002577 CpipJ_CPIJ011605 CpipJ_CPIJ011632 CpipJ_CPIJ016978 GA11162 GA11800 GA12610 All of these are from the insect group. I would like to obtain the fasta CDS for these gen ...
fasta gene ucsc written 5.7 years ago by lin.barnum230 • updated 5.7 years ago by viv_bio30
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Comment: C: Converting A Set Of Protein Ids To Gene Ids
... Thanks, this worked beautifully. ...
written 5.7 years ago by lin.barnum230
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Converting A Set Of Protein Ids To Gene Ids
... I wanted to convert a set of protein IDs to gene IDs. I have a list of proteins IDs such as ADF1_DROME A1Z8K2_DROME A0AQF9_DROME A0AQG1_DROME B4J066_DROGR A0AQG9_DROSI B3NHM7_DROER B3NB45_DROER B3P0U4_DROER B3NJP0_DROER and my final aim is to identify the genes that they originate from since man ...
gene database genes written 5.7 years ago by lin.barnum230 • updated 5.7 years ago by Arnaud Ceol840
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Comment: C: Reverse Read Direction In A Bam File
... Why would the distance between the reads change? ...
written 5.8 years ago by lin.barnum230
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Comment: C: Reverse Read Direction In A Bam File
... Thanks, so would the following gawk script accomplish the reversal of the reads properly? gawk 'BEGIN{OFS="\t"}{if (and($2, 0x40)){$2=xor($2, 0x20)} else if (and($2, 0x80)){$2=xor($2, 0x10)} print $0}' ...
written 5.8 years ago by lin.barnum230
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Reverse Read Direction In A Bam File
... I have a bam alignment file with SOLiD mate-pair data (R3/F3). I want to reverse the second read so that it points towards the first read instead of in the same direction. ------>R3 ------>F3 to ------>R3 <------F3 What I want to know is if it is enough to identify the ...
bam written 5.8 years ago by lin.barnum230 • updated 5.8 years ago by Pierre Lindenbaum120k
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Solid Mate-Pair Alignment With Bwa
... I have aligned SOLiD mate-pair reads using bwa-0.5.9. Now, it is my understanding that SOLiD mate-pair reads are oriented in the same direction R3 ------> F3 ------> I am using a downstream application that expects the reads to be aligned pointing inwards. R3 ------> ...
solid alignment bam written 5.8 years ago by lin.barnum230 • updated 5.8 years ago by Ashutosh Pandey11k
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Comment: C: Large Variation In Base Space Vs Color Space Assembly
... Another question here. How could two different colorspace sequences represent the same basespace sequence? I can see that each colorspace sequence could represent 4 different basespace sequences. A toy example would be useful here. Thanks. ...
written 5.9 years ago by lin.barnum230
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Comment: C: Large Variation In Base Space Vs Color Space Assembly
... While that is true why is the max length and so on different? Shouldn't colorspace be just 1 less than the length of the basespace sequence. ...
written 5.9 years ago by lin.barnum230
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Large Variation In Base Space Vs Color Space Assembly
... I used the pipeline given at Solid Software Tools: DeNovo Assembly/XSQ Tools pipeline mirrored at BioStar to perform a solid assembly. It ran successfully. However, when I look at the statistics of the nucleotide-space assembly and the double-encoded colorspace assembly, they are significantly off. ...
assembly solid velvet written 5.9 years ago by lin.barnum230 • updated 5.9 years ago by Istvan Albert ♦♦ 80k

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