Flag 0 means "the read is not paired and mapped, forward strand".
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Does anybody knows that the value 0 in "SRR087416.97659 0" means? I checked samtools menu, it only says if 0x1 is unset, no assumptions can be made about .....
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my questions was what DNA sequencing platform this output is from, such as Illumina, ABI SOLiD, etc. thanks.
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Thanks for your message.
The result is generated by a Mac Pro with 8GB Memory and 1TB hard drive. Is that you want to know?
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Originally posted by arrchi View PostHi there,
I am looking for a way to find unique hits for my RNA-seq data. After searching online and in this community, I still can't find a good way to find unique hits from a sam file. Any input will be welcome.
I used tophat to align the data to the HG19 and samtools -bq -1 to generated reliable hits.
Here is part of the output:
[Tophat_out]$ grep -w SRR087416.97659 accepted_hits_realiable.sam
SRR087416.97659 0 chr1 11356 1 36M * 0 0 CAGCTAGGGACATTGCAGGGTCCTCTTGCTCAAGGT BBBCBCB9CBBBC@:+>3A97AACABA9@CCCCB9# NM:i:0 NH:i:4 CC:Z:chr12 CP:i:94218
SRR087416.97659 16 chr12 94218 1 36M * 0 0 ACCTTGAGCAAGAGGACCCTGCAATGTCCCTAGCTG #9BCCCC@9ABACAA79A3>+:@CBBBC9BCBCBBB NM:i:0 NH:i:4 CC:Z:chr15 CP:i:102519779
SRR087416.97659 16 chr15 102519779 1 36M * 0 0 ACCTTGAGCAAGAGGACCCTGCAATGTCCCTAGCTG #9BCCCC@9ABACAA79A3>+:@CBBBC9BCBCBBB NM:i:0 NH:i:4 CC:Z:chr2 CP:i:114359624
My questions are: Does this mean that the read SRR087416.97659 maps to chr1, chr12, and chr15?
If I understand the concept "unique-hit" correctly, then this read can not be counted as an unique hit. Am I right?
Thanks,
-A
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unique hits
Hi there,
I am looking for a way to find unique hits for my RNA-seq data. After searching online and in this community, I still can't find a good way to find unique hits from a sam file. Any input will be welcome.
I used tophat to align the data to the HG19 and samtools -bq -1 to generated reliable hits.
Here is part of the output:
[Tophat_out]$ grep -w SRR087416.97659 accepted_hits_realiable.sam
SRR087416.97659 0 chr1 11356 1 36M * 0 0 CAGCTAGGGACATTGCAGGGTCCTCTTGCTCAAGGT BBBCBCB9CBBBC@:+>3A97AACABA9@CCCCB9# NM:i:0 NH:i:4 CC:Z:chr12 CP:i:94218
SRR087416.97659 16 chr12 94218 1 36M * 0 0 ACCTTGAGCAAGAGGACCCTGCAATGTCCCTAGCTG #9BCCCC@9ABACAA79A3>+:@CBBBC9BCBCBBB NM:i:0 NH:i:4 CC:Z:chr15 CP:i:102519779
SRR087416.97659 16 chr15 102519779 1 36M * 0 0 ACCTTGAGCAAGAGGACCCTGCAATGTCCCTAGCTG #9BCCCC@9ABACAA79A3>+:@CBBBC9BCBCBBB NM:i:0 NH:i:4 CC:Z:chr2 CP:i:114359624
My questions are: Does this mean that the read SRR087416.97659 maps to chr1, chr12, and chr15?
If I understand the concept "unique-hit" correctly, then this read can not be counted as an unique hit. Am I right?
Thanks,
-ATags: None
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