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Hi. thank you in advance.
So I am reading through the manual of CNV-seq and have a question with this part:
question: I did not use BLAT or SOLID alignment tools, but used Tophat2 and have the bam file. The manual says that the Best hit perl scripts are ONLY used for BLAT/SOLID alignments. but it also gives a script by Samtools to give map locations with a bam file. So is the samtools command line equivalent to the best_hits.pl scripts?
"We provide best-hit.*.pl for obtaining the best mapping locations for several alignment
tools. Currently it only support BLAT psl file and SOLiD matching pipeline (in
corona_lite) output as input. To extract map locations from a *.bam file (by SAM tools),
try this command:
samtools view -F 4 my.bam | perl -lane 'print "$F[2]\t$F[3]"' > my.hits"
So I am reading through the manual of CNV-seq and have a question with this part:
question: I did not use BLAT or SOLID alignment tools, but used Tophat2 and have the bam file. The manual says that the Best hit perl scripts are ONLY used for BLAT/SOLID alignments. but it also gives a script by Samtools to give map locations with a bam file. So is the samtools command line equivalent to the best_hits.pl scripts?
"We provide best-hit.*.pl for obtaining the best mapping locations for several alignment
tools. Currently it only support BLAT psl file and SOLiD matching pipeline (in
corona_lite) output as input. To extract map locations from a *.bam file (by SAM tools),
try this command:
samtools view -F 4 my.bam | perl -lane 'print "$F[2]\t$F[3]"' > my.hits"
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